Humanized antibodies

ABSTRACT

Disclosed herein are humanized antibodies in which human germline residues are introduces to the complementarity determining regions (CDRs) of a non-human donor antibody. Also described herein are libraries of antibody variable domains (e.g., phage-display libraries) and methods for screening for humanized antibodies.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims the benefit of U.S. provisional application No. 62/162,905, filed May 18, 2016, which is incorporated by reference in its entirety for all purposes.

REFERENCE TO SEQUENCE LISTING

This application contains a Sequence Listing which has been submitted electronically in ASCII format and is hereby incorporated by reference in its entirety. Said ASCII copy, created on May 16, 2016, is named PC72222A_Seq_Listing_ST25.txt and is 367,747 bytes in size.

FIELD OF THE INVENTION

This invention relates to antibody humanization by introducing human germ-line residues in complementarity determining regions (CDRs).

BACKGROUND OF THE INVENTION

Monoclonal antibodies can rapidly be produced by the mouse immune system for biological studies. In a clinical setting, however, the use of these murine antibodies can result in a human anti-mouse antibody response (HAMA). Chimeric antibodies can reduce anti-IgG responses in human, but murine v-domains may still have provocative T-cell epitope content, necessitating “humanization” of their framework regions.

Classical humanization generally begins by transferring all six murine complementarity determining regions (CDRs) onto a human antibody framework (Jones et al., Nature 321, 522-525 (1986)). These CDR-grafted antibodies generally do not retain their original affinity for antigen binding, and in fact, affinity is often severely impaired. Besides the CDRs, certain non-human framework residues must also be incorporated into the variable domains to maintain proper CDR conformation (Chothia et al., Nature 342:877 (1989)). The incorporation of murine residues at key positions in the human frameworks to restore function is generally referred to as “back-mutations.” Back-mutations can support structural conformation of the grafted CDRs and restore antigen binding and affinity. Many of the framework positions that are likely to affect affinity have been identified, thus structural modeling to select new residues in a stepwise fashion can generally lead to variants with restored antigen binding. Alternatively, phage antibody libraries targeted at these residues can also be used to enhance and speed up the affinity maturation process (Wu et al., J. Mol. Biol. 294:151-162 (1999) and Wu, H., Methods in Mol. Biol. 207:197-212 (2003)).

Current humanization techniques still suffer from flaws, such as high non-human amino acid content retention; grafting into poorly understood frameworks; requirement for homology modeling of the v-domains, which is often inaccurate; or a co-crystal structure with the target antigen. Therefore, there is a need to develop new humanization methods.

SUMMARY OF THE INVENTION

Disclosed herein are “ultra” humanized antibodies in which human germline residues are introduced to the complementarity determining regions (CDRs) of a non-human donor antibody. Also described herein are libraries and methods for screening for humanized antibodies.

Those skilled in the art will recognize, or be able to ascertain using no more than routine experimentation, many equivalents to the specific embodiments of the invention described herein. Such equivalents are intended to be encompassed by the following embodiments (E).

E1. A method of generating a library comprising a plurality of polypeptides, for selection of a humanized antibody that binds to a target antigen, comprising:

-   -   (a) obtaining the sequence a non-human donor antibody that binds         to said target antigen, and determining the donor CDR-L1,         CDR-L2, CDR-L3, CDR-H1, and CDR-H2 sequences of said non-human         antibody;     -   (b) obtaining the sequences of a human germline VL and a human         germline VH, and determining the germline framework and germline         CDR-L1, CDR-L2, CDR-L3, CDR-H1, and CDR-H2 sequences of said         human VL and VH;     -   (c) aligning each of the non-human donor CDR-L1, CDR-L2, and         CDR-L3 sequences with the corresponding germline CDR sequence         from said human VL, and each of the non-human CDR-H1 and CDR-H2         sequences with corresponding germline CDR sequence from said         human VH;     -   (d) identifying positions in CDR-L1, CDR-L2, CDR-L3, CDR-H1, and         CDR-H2 where human germline residue is the same as, or different         from, the corresponding non-human donor residue;     -   (e) generating a library of polypeptides, each polypeptide         comprising an antibody variable domain, wherein said antibody         variable domain comprises (1) a VH domain comprising: the         framework sequence of the human germline VH from step (b), and         CDR-H1, CDR-H2, and CDR-H3; and (2) a VL domain comprising: the         framework sequence of the human germline VL from step (b), and         CDR-L1, CDR-L2, and CDR-L3; wherein:         -   (i) for each individual position within CDR-L1, CDR-L2,             CDR-L3, CDR-H1 and CDR-H2:             -   if the human germline residue at said position is the                 same as the corresponding non-human donor residue, all                 polypeptides in the library comprise the human germline                 residue at said position;             -   if the human germline residue at the position is                 different from the corresponding non-human donor                 residue, a portion of the polypeptides in the library                 comprise the human germline residue at said position,                 the remainder of the polypeptides comprise the                 corresponding non-human donor residue at said position;         -   (ii) for each individual position within CDR-H3, the residue             is any one of the 20 natural amino acid residues;         -   (iii) less than 1% of the polypeptides in said library             comprise the original non-human donor CDR-L1, CDR-L2,             CDR-L3, CDR-H1, and CDR-H2 sequences; and         -   (iv) less than 1% of the polypeptides in said library             comprise the original human VL germline CDR-L1, CDR-L2, and             CDR-L3, and the original human VH germline CDR-H1 and CDR-H2             sequences.             E2. The method of embodiment 1, wherein for each individual             position within CDR-L1, CDR-L2, CDR-L3, CDR-H1, and CDR-H2,             if the human germline residue and non-human donor residue             are different according to step (d), the percentage of             polypeptides comprising the human germline residue at said             position is from about 5% to about 95%, the remainder             comprising the corresponding non-human donor residue at said             position.             E3. The method of embodiment 1 or 2, wherein for each             individual position within CDR-L1, CDR-L2, CDR-L3, CDR-H1,             and CDR-H2, if the human germline residue and non-human             donor residue are different according to step (d), the             percentage of polypeptides comprising the human germline             residue at said position is from about 10% to about 90%, the             remainder comprising the corresponding non-human donor             residue at said position.             E4. The method of any one of embodiments 1-3, wherein for             each individual position within CDR-L1, CDR-L2, CDR-L3,             CDR-H1, and CDR-H2, if the human germline residue and             non-human donor residue are different according to step (d),             the percentage of polypeptides comprising the human germline             residue at said position is from about 15% to about 85%, the             remainder comprising the corresponding non-human donor             residue at said position.             E5. The method of any one of embodiments 1-4, wherein for             each individual position within CDR-L1, CDR-L2, CDR-L3,             CDR-H1, and CDR-H2, if the human germline residue and             non-human donor residue are different according to step (d),             the percentage of polypeptides comprising the human germline             residue at said position is from about 20% to about 80%, the             remainder comprising the corresponding non-human donor             residue at said position.             E6. The method of any one of embodiments 1-5, wherein for             each individual position within CDR-L1, CDR-L2, CDR-L3,             CDR-H1, and CDR-H2, if the human germline residue and             non-human donor residue are different according to step (d),             the percentage of polypeptides comprising the human germline             residue at said position is from about 25% to about 75%, the             remainder comprising the corresponding non-human donor             residue at said position.             E7. The method of any one of embodiments 1-6, wherein for             each individual position within CDR-L1, CDR-L2, CDR-L3,             CDR-H1, and CDR-H2, if the human germline residue and             non-human donor residue are different according to step (d),             the percentage of polypeptides comprising the human germline             residue at said position is from about 30% to about 70%, the             remainder comprising the corresponding non-human donor             residue at said position.             E8. The method of any one of embodiments 1-7, wherein for             each individual position within CDR-L1, CDR-L2, CDR-L3,             CDR-H1, and CDR-H2, if the human germline residue and             non-human donor residue are different according to step (d),             the percentage of polypeptides comprising the human germline             residue at said position is from about 35% to about 65%, the             remainder comprising the corresponding non-human donor             residue at said position.             E9. The method of any one of embodiments 1-8, wherein for             each individual position within CDR-L1, CDR-L2, CDR-L3,             CDR-H1, and CDR-H2, if the human germline residue and             non-human donor residue are different according to step (d),             the percentage of polypeptides comprising the human germline             residue at said position is from about 40% to about 60%, the             remainder comprising the corresponding non-human donor             residue at said position.             E10. The method of any one of embodiments 1-9, wherein for             each individual position within CDR-H3, each of the 20             natural amino acid residues is represented by at least about             0.1% of the polypeptides in the library.             E11. The method of any one of embodiments 1-10, wherein for             each individual position within CDR-H3, each of the 20             natural amino acid residues is represented by at least about             1% of the polypeptides in the library.             E12. The method of any one of embodiments 1-11, wherein for             each individual position within CDR-H3, each of the 20             natural amino acid residues is represented by at least about             2% of the polypeptides in the library.             E13. The method of any one of embodiments 1-12, wherein for             each individual position within CDR-H3, each of the 20             natural amino acid residues is represented by from about 2%             to about 8% of the polypeptides in the library.             E14. A method of humanizing a non-human donor antibody,             wherein said non-human donor antibody binds to a target             antigen, comprising:     -   (a) obtaining the sequence said non-human donor antibody, and         determining the donor CDR-L1, CDR-L2, CDR-L3, CDR-H1, CDR-H2,         and CDR-H3 sequences;     -   (b) obtaining the sequences of a human germline VL and a human         germline VH, and determining the germline framework and germline         CDR-L1, CDR-L2, CDR-L3, CDR-H1, and CDR-H2 sequences of said         human VL and VH;     -   (c) aligning each of the non-human donor CDR-L1, CDR-L2, and         CDR-L3 sequences with the corresponding germline CDR sequence         from said human VL, and each of the non-human CDR-H1 and CDR-H2         sequences with corresponding germline CDR sequence from said         human VH;     -   (d) identifying positions in CDR-L1, CDR-L2, CDR-L3, CDR-H1, and         CDR-H2 where human germline residue is or different from the         corresponding non-human donor residue;     -   (e) obtaining a humanized antibody by:         -   (i) grafting said non-human donor CDR-L1, CDR-L2, and CDR-L3             into said human VL germline framework, and said non-human             donor CDR-H1, CDR-H2, CDR-H3 into said human VH germline             framework; and         -   (ii) further introducing a mutation in at least one, but not             all, of the positions identified in (d), wherein said             mutation comprises replacing a non-human donor residue with             the corresponding human germline residue;         -   (iii) introducing at least one random mutation in CDR-H3,             wherein said mutation comprises replacing a non-human donor             residue with a different amino acid residue;     -   (f) assessing the binding affinity of the humanized antibody         obtained in (e) to the target antigen.         E15. The method of embodiment 14, comprising introducing         mutations in at least three, but not all, of the positions         identified in (d), wherein said mutations comprise replacing a         non-human donor residue with the corresponding human germline         residue.         E16. The method of embodiment 14 or 15, comprising introducing         mutations in at least five, but not all, of the positions         identified in (d), wherein said mutations comprise replacing a         non-human donor residue with the corresponding human germline         residue.         E17. The method of any one of embodiments 14-16, comprising         introducing two or more random mutations in CDR-H3, wherein said         mutations comprise replacing a non-human donor residue with a         different amino acid residue.         E18. The method of any one of embodiments 1-17, wherein said         human germline VH framework sequence comprises a VH3 framework         sequence.         E19. The method of any one of embodiments 1-17, wherein said         human germline VH framework sequence comprises a VH1 framework         sequence.         E20. The method of any one of embodiments 1-17, wherein said         human germline VH framework sequence comprises a VH5 framework         sequence.         E21. The method of any one of embodiments 1-17, wherein said         human germline VH framework sequence comprises the VH framework         sequence of any one of the human germline sequences listed in         Table 2.         E22. The method of any one of embodiments 1-17 and 21, wherein         said human germline VH framework sequence comprises the VH         framework sequence of human germline IGHV3-23 or IGHV1-69.         E23. The method of any one of embodiments 1-17 and 21, wherein         said human germline VH framework sequence comprises the VH         framework sequence of human germline IGHV3-7.         E24. The method of any one of embodiments 1-17, wherein said         human germline VH framework sequence comprises a VH germline         consensus framework sequence.         E25. The method of embodiment 24, wherein said human germline VH         framework sequence comprises the VH framework sequence of any         one of the consensus sequences listed in Table 5.         E26. The method of any one of embodiments 1-25, wherein said         human germline VL framework sequence comprises a V_(K) framework         sequence.         E27. The method of any one of embodiments 1-26, wherein said         human germline VL framework sequence comprises the VL framework         sequence of any one of the human germline sequences listed in         Table 3.         E28. The method of any one of embodiments 1-25 wherein said         human germline VL framework sequence comprises a V_(λ) framework         sequence.         E29. The method of any one of embodiments 1-25 and 28, wherein         said human germline VL framework sequence comprises the VL         framework sequence of any one of the human germline sequences         listed in Table 4.         E30. The method of any one of embodiments 1-25, wherein said         human germline VL framework sequence comprises the VL framework         sequence of human germline IGKV3-20.         E31. The method of any one of embodiments 1-25, wherein said         human germline VL framework sequence comprises the VL framework         sequence of human germline IGKV1-39.         E32. The method of any one of embodiments 1-25, wherein said         human germline VL framework sequence comprises a VL germline         consensus framework sequence.         E33. The method of any one of embodiments 1-25 and 32, wherein         said human germline VL framework sequence comprises the VL         framework sequence of any one of consensus sequences listed in         Table 6.         E34. The method of any one of embodiments 1-33, wherein said         non-human donor antibody is a non-human mammalian antibody.         E35. The method of any one of embodiments 1-34, wherein said         non-human donor antibody is a murine antibody, a rat antibody,         or a rabbit antibody.         E36. The method of any one of embodiments 1-35, wherein said         non-human donor antibody is a murine antibody.         E37. The method of any one of embodiments 34-36, wherein said         human germline VL framework comprises no more than 3         back-mutations or random mutations.         E38. The method of any one of embodiments 34-37, wherein said         human germline VH framework comprises no more than 3         back-mutations or random mutations.         E39. The method of any one of embodiments 34-38, wherein said         human germline VL framework and VH framework together comprise         no more than 3 back-mutations or random mutations.         E40. The method of any one of embodiments 34-39, wherein at         least one back-mutation or random mutation is located between         heavy chain residues H71 to H80.         E41. The method of any one of embodiments 34-39, wherein said         human germline VH framework and human germline VH framework do         not comprise a back-mutation.         E42. The method of any one of embodiments 1-33, wherein said         non-human donor antibody is an avian antibody.         E43. The method of embodiment 42, wherein said human germline VL         framework comprises no more than 5 back-mutations or random         mutations.         E44. The method of embodiment 42 or 43, wherein said human         germline VH framework comprises no more than 5 back-mutations or         random mutations.         E45. The method of any one of embodiments 42-44, wherein said         human germline VL framework and VH framework together comprise         no more than 5 back-mutations or random mutations.         E46. The method of any one of embodiments 42-45, wherein at         least one back-mutation or random mutation is located between         heavy chain residues H71 to H80.         E47. The method of any one of embodiments 42-45, wherein said         human germline VL framework comprises a single back-mutation.         E48. The method of any one of embodiments 42-46, wherein said         human germline VH framework comprises a single back-mutation.         E49. The method of any one of embodiments 42-47, wherein said         non-human donor antibody is a chicken antibody.         E50. The method of any one of embodiments 42-45 and 47-49,         wherein said human germline VL framework comprises a         back-mutation at position 46 (such as Leu46Thr (L46T)).         E51. The method of any one of embodiments 1-13 and 18-50,         wherein said library is a phage display library.         E52. The method of any one of embodiments 1-51, further         comprising: obtaining the sequence of a human germline VH         by: (i) aligning the framework sequence of said non-human donor         antibody VH against a plurality of human germline VH framework         sequences; and (ii) selecting a human germline VH framework that         has the highest sequence identity according to step (i).         E53. The method of any one of embodiments 1-52, further         comprising: obtaining the sequence of a human germline VL         by: (i) aligning the framework sequence of said non-human donor         antibody VL against a plurality of human germline VL framework         sequences; and (ii) selecting a human germline VL framework that         has the highest sequence identity according to step (i).         E54. A library for humanizing a non-human donor antibody that         binds to a target antigen, wherein:     -   (a) said library comprises a plurality of polypeptides, each         polypeptide comprising an antibody variable domain;     -   (b) said antibody variable domain comprises (i) a VH domain         comprising: a human germline VH framework sequence, and CDR-H1,         CDR-H2, and CDR-H3;     -   and (ii) a VL domain comprising: a human germline VL framework         sequence, and CDR-L1, CDR-L2, and CDR-L3;     -   (c) for each individual position within said CDR-L1, CDR-L2,         CDR-L3, CDR-H1, and CDR-H2,         -   if the human germline residue at said position is the same             as the corresponding non-human donor residue, all             polypeptides in the library comprise the human germline             residue at said position;         -   if the human germline residue at the position is different             from the corresponding non-human donor residue, a portion of             the polypeptides in the library comprise the human germline             residue at said position, the remainder of the polypeptides             comprise the corresponding non-human donor residue at said             position;     -   (d) for each individual position within CDR-H3, the residue is         any one of the natural amino acid residues;     -   (e) less than 1% of the polypeptides in said library comprise         the original non-human donor CDR-L1, CDR-L2, CDR-L3, CDR-H1, and         CDR-H2 sequences; and     -   (f) less than 1% of the polypeptides in said library comprise         the original human VL germline CDR-L1, CDR-L2, and CDR-L3, and         the original human VH germline CDR-H1 and CDR-H2 sequences.         E55. The library of embodiment 54, wherein for each individual         position within CDR-L1, CDR-L2, CDR-L3, CDR-H1, and CDR-H2, if         the human germline residue and non-human donor residue are         different at said position, the percentage of polypeptides         comprising the human germline residue at said position is from         about 5% to about 95%, the remainder comprising the         corresponding non-human donor residue at said position.         E56. The library of embodiment 54 or 55, wherein for each         individual position within CDR-L1, CDR-L2, CDR-L3, CDR-H1, and         CDR-H2, if the human germline residue and non-human donor         residue are different at said position, the percentage of         polypeptides comprising the human germline residue at said         position is from about 10% to about 90%, the remainder         comprising the corresponding non-human donor residue at said         position.         E57. The library of any one of embodiments 54-56, wherein for         each individual position within CDR-L1, CDR-L2, CDR-L3, CDR-H1,         and CDR-H2, if the human germline residue and non-human donor         residue are different at said position, the percentage of         polypeptides comprising the human germline residue at said         position is from about 15% to about 85%, the remainder         comprising the corresponding non-human donor residue at said         position.         E58. The library of any one of embodiments 54-57, wherein for         each individual position within CDR-L1, CDR-L2, CDR-L3, CDR-H1,         and CDR-H2, if the human germline residue and non-human donor         residue are different at said position, the percentage of         polypeptides comprising the human germline residue at said         position is from about 20% to about 80%, the remainder         comprising the corresponding non-human donor residue at said         position.         E59. The library of any one of embodiments 54-58, wherein for         each individual position within CDR-L1, CDR-L2, CDR-L3, CDR-H1,         and CDR-H2, if the human germline residue and non-human donor         residue are different at said position, the percentage of         polypeptides comprising the human germline residue at said         position is from about 25% to about 75%, the remainder         comprising the corresponding non-human donor residue at said         position.         E60. The library of any one of embodiments 54-59, wherein for         each individual position within CDR-L1, CDR-L2, CDR-L3, CDR-H1,         and CDR-H2, if the human germline residue and non-human donor         residue are different at said position, the percentage of         polypeptides comprising the human germline residue at said         position is from about 30% to about 70%, the remainder         comprising the corresponding non-human donor residue at said         position.         E61. The library of any one of embodiments 54-60, wherein for         each individual position within CDR-L1, CDR-L2, CDR-L3, CDR-H1,         and CDR-H2, if the human germline residue and non-human donor         residue are different at said position, the percentage of         polypeptides comprising the human germline residue at said         position is from about 35% to about 65%, the remainder         comprising the corresponding non-human donor residue at said         position.         E62. The library of any one of embodiments 54-61, wherein for         each individual position within CDR-L1, CDR-L2, CDR-L3, CDR-H1,         and CDR-H2, if the human germline residue and non-human donor         residue are different at said position, the percentage of         polypeptides comprising the human germline residue at said         position is from about 40% to about 60%, the remainder         comprising the corresponding non-human donor residue at said         position.         E63. The library of any one of embodiments 54-62, wherein for         each individual position within CDR-H3, each of the 20 natural         amino acid residues is represented by at least about 0.1% of the         polypeptides in the library.         E64. The library of any one of embodiments 54-63, wherein for         each individual position within CDR-H3, each of the 20 natural         amino acid residues is represented by at least about 1% of the         polypeptides in the library.         E65. The library of any one of embodiments 54-64, wherein for         each individual position within CDR-H3, each of the 20 natural         amino acid residues is represented by at least about 2% of the         polypeptides in the library.         E66. The library of any one of embodiments 54-65, wherein for         each individual position within CDR-H3, each of the 20 natural         amino acid residues is represented by from about 2% to about 8%         of the polypeptides in the library.         E67. The library of any one of embodiments 54-66, wherein said         human germline VH framework sequence comprises a VH3 framework         sequence.         E68. The library of any one of embodiments 54-66, wherein said         human germline VH framework sequence comprises a VH1 framework         sequence.         E69. The library of any one of embodiments 54-66, wherein said         human germline VH framework sequence comprises a VH5 framework         sequence.         E70. The library of any one of embodiments 54-66, wherein said         human germline VH framework sequence comprises the VH framework         sequence of any one of the human germline sequences listed in         Table 2.         E71. The library of any one of embodiments 54-66 and 70, wherein         said human germline VH framework sequence comprises the VH         framework sequence of human germline IGHV3-23 or IGHV1-69.         E72. The library of any one of embodiments 54-66 and 70, wherein         said human germline VH framework sequence comprises the VH         framework sequence of human germline IGHV3-7.         E73. The library of any one of embodiments 54-66, wherein said         human germline VH framework sequence comprises a VH germline         consensus framework sequence.         E74. The library of embodiment 73, wherein said human germline         VH framework sequence comprises the VH framework sequence of any         one of the consensus sequences listed in Table 5.         E75. The library of any one of embodiments 54-74, wherein said         human germline VL framework sequence comprises a V_(K) framework         sequence.         E76. The library of any one of embodiments 54-75, wherein said         human germline VL framework sequence comprises the VL framework         sequence of any one of the human germline sequences listed in         Table 3.         E77. The library of any one of embodiments 54-74, wherein said         human germline VL framework sequence comprises a V_(λ) framework         sequence.         E78. The library of any one of embodiments 54-74 and 77, wherein         said human germline VL framework sequence comprises the VL         framework sequence of any one of the human germline sequences         listed in Table 4.         E79. The library of any one of embodiments 54-74, wherein said         human germline VL framework sequence comprises the VL framework         sequence of human germline IGKV3-20.         E80. The library of any one of embodiments 54-74, wherein said         human germline VL framework sequence comprises the VL framework         sequence of human germline IGKV1-39.         E81. The library of any one of embodiments 54-74, wherein said         human germline VL framework sequence comprises a VL germline         consensus framework sequence.         E82. The library of any one of embodiments 54-74 and 81, wherein         said human germline VL framework sequence comprises the VL         framework sequence of any one of consensus sequences listed in         Table 6.         E83. The library of any one of embodiments 54-82, wherein said         non-human donor antibody is a non-human mammalian antibody.         E84. The library of any one of embodiments 54-83, wherein said         non-human donor antibody is a murine antibody, a rat antibody,         or a rabbit antibody.         E85. The library of any one of embodiments 54-84, wherein said         non-human donor antibody is a murine antibody.         E86. The library of any one of embodiments 83-85, wherein said         human germline VL framework comprises no more than 3         back-mutations or random mutations.         E87. The library of any one of embodiments 83-86, wherein said         human germline VH framework comprises no more than 3         back-mutations or random mutations.         E88. The library of any one of embodiments 83-87, wherein said         human germline VL framework and VH framework together comprise         no more than 3 back-mutations or random mutations.         E89. The library of any one of embodiments 83-88, wherein at         least one back-mutation or random mutation is located between         heavy chain residues H71 to H80.         E90. The library of any one of embodiments 83-88, wherein said         human germline VH framework and human germline VH framework do         not comprise a back-mutation.         E91. The library of any one of embodiments 54-82, wherein said         non-human donor antibody is an avian antibody.         E92. The library of embodiment 91, wherein said human germline         VL framework comprises no more than 5 back-mutations or random         mutations.         E93. The library of embodiment 91 or 92, wherein said human         germline VH framework comprises no more than 5 back-mutations or         random mutations.         E94. The library of any one of embodiments 91-93, wherein said         human germline VL framework and VH framework together comprise         no more than 5 back-mutations or random mutations.         E95. The library of any one of embodiments 91-94, wherein at         least one back-mutation or random mutation is located between         heavy chain residues H71 to H80.         E96. The library of any one of embodiments 91-95, wherein said         human germline VL framework comprises a single back-mutation.         E97. The library of any one of embodiments 91-96, wherein said         human germline VH framework comprises a single back-mutation.         E98. The library of any one of embodiments 91-97, wherein said         non-human donor antibody is a chicken antibody.         E99. The library of any one of embodiments 91-94 and 96-98,         wherein said human germline VL framework comprises a         back-mutation at position 46 (such as Leu46Thr (L46T).         E100. The library of any one of embodiments 54-99, wherein said         library is a phage display library.         E101. A plurality of nucleic acid molecules encoding the library         of any one of embodiments 54-100.         E102. The plurality of nucleic acid molecules of embodiment 101,         wherein said nucleic acid molecules are phagemid vectors.         E103. A plurality of host cells comprising the nucleic acid         molecules of embodiment 101 or 102.         E104. A method of identifying an antibody variable domain         sequence that binds to a target antigen, comprising:     -   (a) obtaining the library of any one of embodiments 54-100;     -   (b) selecting a polypeptide that binds to said target antigen,         with an affinity (Kd) value of 5×10⁻⁵ M or less, and     -   (c) obtaining the sequence of the antibody variable domain of         the polypeptide selected in step (b).         E105. The method of embodiment 104, wherein said an antibody         variable domain binds to said target antigen with a binding         affinity (Kd) value that is equal or less than that of said         non-human donor antibody.         E106. The method of embodiment 104 or 105, further comprising         producing a nucleic acid vector encoding a polypeptide         comprising the antibody variable domain selected from step (c).         E107. The method of embodiment 106, further comprising         introducing said vector into a host cell.         E108. The method of embodiment 106 or 107, wherein said vector         is an expression vector.         E109. The method of embodiment 107 or 108, further comprising         culturing said host cell in a medium under a suitable condition,         such that said polypeptide is expressed.         E110. The method of embodiment 109, further comprising         harvesting said polypeptide from the medium.         E111. The method of embodiment 110, further comprising purifying         said polypeptide.         E112. A humanized antibody or antigen-binding fragment thereof         that binds to a target antigen, wherein:     -   (a) said antibody or antigen-binding fragment thereof         comprises (i) a VH domain comprising: a human germline VH         framework sequence, and CDR-H1, CDR-H2, and CDR-H3; and (ii) a         VL domain comprising: a human germline VL framework sequence,         and CDR-L1, CDR-L2, and CDR-L3;     -   (b) said CDR-L1, CDR-L2, CDR-L3, CDR-H1, and CDR-H2 are derived         from corresponding CDRs from a non-human donor antibody that         binds to said target antigen;     -   (c) for each position within said CDR-L1, CDR-L2, CDR-L3,         CDR-H1, and CDR-H2, the residue is either human germline residue         from said human germline VL or VH, or corresponding residue from         said non-human donor antibody;     -   (d) said CDR-L1, CDR-L2, CDR-L3, CDR-H1, and CDR-H2 each         comprises at least one more human germline residue as compared         to the corresponding non-human donor CDR,     -   (e) said CDR-L1, CDR-L2, CDR-L3, CDR-H1, and CDR-H2 each         comprises at least one more non-human donor residue as compared         to the corresponding human germline VH or VL CDR; and     -   (f) for each position within CDR-H3, the residue is any one of         the 20 natural amino acid residues.         E113. The antibody or antigen-binding fragment of embodiment         112, wherein said antibody or antigen-binding fragment binds to         said target antigen with a binding affinity (Kd) value of 5×10⁻⁵         M or less.         E114. The antibody or antigen-binding fragment of embodiment 112         or 113, wherein said antibody or antigen-binding fragment binds         said target antigen with a binding affinity (Kd) value that is         equal or less than the binding affinity (Kd) value of said         non-human donor antibody.         E115. The antibody or antigen-binding fragment of any one of         embodiments 112-114, wherein said human germline VH framework         sequence comprises a VH3 framework sequence.         E116. The antibody or antigen-binding fragment of any one of         embodiments 112-114, wherein said human germline VH framework         sequence comprises a VH1 framework sequence.         E117. The antibody or antigen-binding fragment of any one of         embodiments 112-114, wherein said human germline VH framework         sequence comprises a VH5 framework sequence.         E118. The antibody or antigen-binding fragment of any one of         embodiments 112-114, wherein said human germline VH framework         sequence comprises the VH framework sequence of any one of the         human germline sequences listed in Table 2.         E119. The antibody or antigen-binding fragment of any one of         embodiments 112-114 and 118, wherein said human germline VH         framework sequence comprises the VH framework sequence of human         germline IGHV3-23 or IGHV1-69.         E120. The antibody or antigen-binding fragment of any one of         embodiments 112-114 and 118, wherein said human germline VH         framework sequence comprises the VH framework sequence of human         germline IGHV3-7.         E121. The antibody or antigen-binding fragment thereof of any         one of embodiments 112-114, wherein said human germline VH         framework sequence comprises a VH germ line consensus framework         sequence.         E122. The antibody or antigen-binding fragment thereof of         embodiment 121, wherein said human germline VH framework         sequence comprises the VH framework sequence of any one of the         consensus sequences listed in Table 5.         E123. The antibody or antigen-binding fragment thereof of any         one of embodiments 112-122, wherein said human germline VL         framework sequence comprises a V_(K)framework sequence.         E124. The antibody or antigen-binding fragment thereof of any         one of embodiments 112-123, wherein said human germline VL         framework sequence comprises the VL framework sequence of any         one of the human germline sequences listed in Table 3.         E125. The antibody or antigen-binding fragment thereof of any         one of embodiments 112-122 wherein said human germline VL         framework sequence comprises a V_(λ) framework sequence.         E126. The antibody or antigen-binding fragment thereof of any         one of embodiments 112-122 and 125, wherein said human germline         VL framework sequence comprises the VL framework sequence of any         one of the human germline sequences listed in Table 4.         E127. The antibody or antigen-binding fragment thereof of any         one of embodiments 112-122, wherein said human germline VL         framework sequence comprises the VL framework sequence of human         germline IGKV3-20.         E128. The antibody or antigen-binding fragment thereof of any         one of embodiments 112-122, wherein said human germline VL         framework sequence comprises the VL framework sequence of human         germline IGKV1-39.         E129. The antibody or antigen-binding fragment thereof of any         one of embodiments 112-122, wherein said human germline VL         framework sequence comprises a VL germline consensus framework         sequence.         E130. The antibody or antigen-binding fragment thereof of any         one of embodiments 112-122 and 129, wherein said human germline         VL framework sequence comprises the VL framework sequence of any         one of consensus sequences listed in Table 6.         E131. The antibody or antigen-binding fragment thereof of any         one of embodiments 112-130, wherein said non-human donor         antibody is a non-human mammalian antibody.         E132. The antibody or antigen-binding fragment thereof of any         one of embodiments 112-131, wherein said non-human donor         antibody is a murine antibody, a rat antibody, or a rabbit         antibody.         E133. The antibody or antigen-binding fragment thereof of any         one of embodiments 112-132, wherein said non-human donor         antibody is a murine antibody.         E134. The antibody or antigen-binding fragment thereof of any         one of embodiments 112-133, wherein said human germline VL         framework comprises no more than 3 back-mutations or random         mutations.         E135. The antibody or antigen-binding fragment thereof of any         one of embodiments 131-134, wherein said human germline VH         framework comprises no more than 3 back-mutations or random         mutations.         E136. The antibody or antigen-binding fragment thereof of any         one of embodiments 131-135, wherein said human germline VL         framework and VH framework together comprise no more than 3         back-mutations or random mutations.         E137. The antibody or antigen-binding fragment thereof of any         one of embodiments 131-136, wherein at least one back-mutation         or random mutation is located between heavy chain residues H71         to H80.         E138. The antibody or antigen-binding fragment thereof of any         one of embodiments 131-136, wherein said human germline VH         framework and human germline VH framework do not comprise a         back-mutation.         E139. The antibody or antigen-binding fragment thereof of any         one of embodiments 112-130, wherein said non-human donor         antibody is an avian antibody.         E140. The antibody or antigen-binding fragment thereof of         embodiment 139, wherein said human germline VL framework         comprises no more than 5 back-mutations or random mutations.         E141. The antibody or antigen-binding fragment thereof of         embodiment 139 or 140, wherein said human germline VH framework         comprises no more than 5 back-mutations or random mutations.         E142. The antibody or antigen-binding fragment thereof of any         one of embodiments 139-141, wherein said human germline VL         framework and VH framework together comprise no more than 5         back-mutations or random mutations.         E143. The antibody or antigen-binding fragment thereof of any         one of embodiments 139-142, wherein at least one back-mutation         or random mutation is located between heavy chain residues H71         to H80.         E144. The antibody or antigen-binding fragment thereof of any         one of embodiments 139-143, wherein said human germline VL         framework comprises a single back-mutation.         E145. The antibody or antigen-binding fragment thereof of any         one of embodiments 139-144, wherein said human germline VH         framework comprises a single back-mutation.         E146. The antibody or antigen-binding fragment thereof of any         one of embodiments 139-145, wherein said non-human donor         antibody is a chicken antibody.         E147. The antibody or antigen-binding fragment thereof of any         one of embodiments 139-142 and 144-146, wherein said human         germline VL framework comprises a back-mutation at light chain         position 46 (such as Leu46Thr (L46T)).         E148. The antibody or antigen-binding fragment of any one of         embodiments 112-147, wherein position 24 of CDR-L1 comprises the         corresponding human germline residue from said human VL         germline.         E149. The antibody or antigen-binding fragment of any one of         embodiments 112-148, wherein position 25 of CDR-L1 comprises the         corresponding human germline residue from said human VL         germline.         E150. The antibody or antigen-binding fragment of any one of         embodiments 112-149, wherein position 26 of CDR-L1 comprises the         corresponding human germline residue from said human VL         germline.         E151. The antibody or antigen-binding fragment of any one of         embodiments 112-150, wherein position 27 of CDR-L1 comprises the         corresponding human germline residue from said human VL         germline.         E152. The antibody or antigen-binding fragment of any one of         embodiment 148-151, wherein said human germline VL is a VK         germline.         E153. The antibody or antigen-binding fragment of any one of         embodiments 112-152, wherein position 60 of CDR-H2 comprises the         corresponding human germline residue from said human VH         germline.         E154. The antibody or antigen-binding fragment of any one of         embodiments 112-153, wherein position 61 of CDR-H2 comprises the         corresponding human germline residue from said human VH         germline.         E155. The antibody or antigen-binding fragment of any one of         embodiments 112-154, wherein position 62 of CDR-H2 comprises the         corresponding human germline residue from said human VH         germline.         E156. The antibody or antigen-binding fragment of any one of         embodiments 112-155, wherein position 63 of CDR-H2 comprises the         corresponding human germline residue from said human VH         germline.         E157. The antibody or antigen-binding fragment of any one of         embodiments 112-156, wherein position 64 of CDR-H2 comprises the         corresponding human germline residue from said human VH         germline.         E158. The antibody or antigen-binding fragment of any one of         embodiments 112-157, wherein position 65 of CDR-H2 comprises the         corresponding human germline residue from said human VH         germline.         E159. The antibody or antigen-binding fragment of any one of         embodiment 153-158, wherein said human germline VH is a VH3         germline.         E160. The antibody or antigen-binding fragment of any one of         embodiment 153-158, wherein said human germline VH is a VH1         germline.         E161. The antibody or antigen-binding fragment of any one of         embodiment 153-158, wherein said human germline VH is a VH5         germline.         E162. The antibody or antigen-binding fragment of any one of         embodiment 153-158, wherein said human germline VH is a VH4         germline.         E163. A nucleic acid molecule encoding the antibody or         antigen-binding fragment thereof of any one of embodiments         112-162.         E164. A host cell comprising the nucleic acid molecule of         embodiment 163.         E165. The host cell of embodiment 164, wherein said host cell is         a CHO cell, a HEK cell, or an Sp2.0 cell.         E166. A method of making an antibody or antigen-binding fragment         thereof, comprising culturing the host cell of embodiment 163 or         164 under a condition wherein said antibody or antigen-binding         fragment is expressed by said host cell.         E167. An antibody or antigen-binding fragment thereof obtained         by the method of any one of embodiments 1-53, 104-111, and 166.         E168. An antibody or antigen-binding fragment thereof obtained         using the library of any one of embodiments 54-100.         E169. A kit comprising the library of any one of embodiments         54-100.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a schematic illustration of ABS library design, selection and screening principles. (A) Amino acid sequences are shown for the v-domains of Par-RAGE and destination germline (DPK9-DP54) scFvs in VL-VH format. At each position where the rat and human residues differed, both residues were encoded for in the ABS-RAGE library (human residue on top and rat residue at bottom). This principle was applied to all CDRs other than the CDR-H3, in a single combinatorial library. In the CDR-H3, point mutations were permitted at a frequency of 1±1 per clone. (B) Phage libraries were generated and (C) used in selections on cognate antigen. (D) Selection output clones were subsequently screened by ELISA, HTRF and DNA sequencing to identify hits with maintained target binding and epitope specificity. (E) Top clones were cloned as IgGs, expressed and purified, before (F) characterization of affinity by Biacore, solubility and aggregation analyses by SEC, in vitro specificity by ELISA and Biacore, and thermal stability analysis by DSC. Human and rat CDR-L1: SEQ ID NOs: 1 and 2, respectively; Human and rat CDR-L2: SEQ ID NOs: 3 and 4, respectively; Human and rat CDR-L3: SEQ ID NOs: 5 and 6, respectively; Human and rat CDR-H1: SEQ ID NOs: 7 and 8, respectively; Human and rat CDR-H2: SEQ ID NOs: 9 and 10, respectively; rat CDR-H3: SEQ ID NO: 11.

FIGS. 2A-2C show the results of biophysical analyses for ABS-derived clones. DSC analysis of IgG thermal stability for anti-RAGE (A), anti-pTau (B) and anti-A33 (C) antibodies. FIGS. 2D-2F show the results of forced IgG aggregation analysis for anti-RAGE (D), anti-pTau (E) and anti-A33 (F) antibodies.

FIGS. 3A-3C show the assessment of potential immunogenicity and level of human identity in the v-domains of ABS-derived leads. (A) EpiMatrix was used to estimate the potential for T-cell epitope driven immunogenicity in the v-domains of C21-ABS-pTau, C2-ABS-A33 and C7-ABS-RAGE in comparison to 31 FDA-approved therapeutic antibodies that are rodent, humanized or “fully human” in sequence. Lower score suggests lower predicted immunogenicity. (B) Comparison of non-human solvent-accessible surface area (nhSASA, in Å²) that contributed to the v-domains of parental (black), grafted (grey) and ABS (white) clones for pTau, A33 and RAGE. While CDR grafting dramatically lowers the nhSASA score in all cases, the ABS lead clones all exhibit minimized exposure of non-human amino acid motifs that might constitute b-cell epitopes. (C) Publically available, online tools which estimate levels of v-gene sequence identity to the human v-domain repertoire were used to calculate T20, Z and G scores for 31 approved therapeutic antibodies that are rodent, humanized or “fully human” in origin, plus the parental, graft (triangles) and ABS leads for pTau (black squares), RAGE (stars) and A33 (diamonds).

FIGS. 4A-4B show CDR redundancy analyses in anti-pTau via mutational tolerance analysis. A plot of chicken amino acid retention frequencies in the CDRs of the ELISA-positive population of 188 unique clones from ABS-pTau library screening is shown for (A) V_(H) and (B) V_(L) domains, respectively. Only those residues targeted for binary human/chicken substitution are plotted. CDR residues noted on the X-axis whose values are set at 0 were identical human-chicken and not sampled in the library, but are included in the figure for clarity (e.g G26-). In both plots the mean human-chicken frequency (˜50%) in sequenced clones from the starting library is plotted as a dashed line, with standard deviations as solid bold lines. Residues predicted to be making antigen contacts in a co-crystal structural analysis that were also retained at >80% (i.e. where mutational tolerance was low) are highlighted with striped bars. Predicted contact residues not found to be retained are highlighted in checked bars.

FIGS. 5A-5C show ELISA analyses of scFv function after expression in E. coli from phagemid vector pWRIL-1. Binding signals in titration ELISA against: (A) pT231_pS235 peptide for purified V_(L)-V_(H) scFv forms of Par-pTau and Graft-pTau. (B) hRAGE and mRAGE for periprep V_(L)-V_(H) scFv forms of CL-Hum-pTau and Graft-RAGE. (C) Human A33 ectodomain protein for purified V_(L)-V_(H) scFv forms of Par-A33 and Graft-A33. In all cases (A-C), the grafted scFvs show significantly impaired binding activity.

FIG. 6 shows sequence alignments for V_(L) and V_(H) domains of 8 prioritized lead clones from the ABS-pTau library (from top to bottom, SEQ ID NOs. 12-29). CDR regions are boxed in grey. Amino acids differing from the human DPL16/JL2 and DP47/JH4 germlines are underlined. Black arrow indicates the position of the L46T mutation positively selected in the FW2 of all clones showing functional binding to target.

FIGS. 7A-7C show the IgG titration HTRF data for representative lead ABS-derived clones prioritized on the basis of: % reduction in parental residue CDR content and neutralisation of parental IgG binding to antigen, with the change in fluorescence intensity relative to baseline (F/F0) IC₅₀ values approximately equivalent to or better than parental IgG. (A) Anti-pTau clones, (B) Anti-RAGE clones, (C) Anti-A33 clones (-ve control non-A33-specific IgG added instead of graft due to graft expression problems).

FIGS. 8A-8D show the results of IgG specificity testing.

FIG. 9 shows in silico predictions for T-cell epitopes within the full V_(H) and V_(L) regions of lead clones were performed with EpiMatrix (Epivax, RI) (from top to bottom, SEQ ID NOs. 30-49, 45, 50-52, 30, 53-55). Possible epitopes are defined as 9-mer sequences with four or more hits and are shown based on potential epitopes different to human germ-line, potential epitopes in germ-line sequence to which most patients should exhibit self-tolerance, and epitopes in germ-line sequence reported to be potential t-regulatory cell stimulating sequences. Where potential epitopes overlap the coloring of the C-terminal epitope is used. C7-ABS-RAGE has the lowest immunogenicity potential of the anti-RAGE clones as it contains 2 potential t-cell epitopes and 13 potential t-regitopes, in comparison to 9 potential t-cell epitopes and only one t-regitope in Par-RAGE and 2 potential t-cell epitopes with 10 potential t-regitopes in CL-Hum-RAGE. Notably, the ABS germlining of the c-terminal end of the CDR-H2 (VKD>VKG) reinstates a potential germline t-regitope, as does the germlining of the V_(L) FW2. Similarly, C21-ABS-pTau has the lowest immunogenicity potential of the anti-pTau clones as it contains only 1 potential t-cell epitope and 9 potential t-regitopes, in comparison to 5 potential t-cell epitopes and only one t-regitope in Par-pTau and 2 potential t-cell epitopes with 9 potential t-regitopes in Graft-pTau.

FIGS. 10A-10C are retention frequency plots for all positions across 5 CDR-humanized antibodies (A33, pTau, BDNF, IL33, and FN14) using the ABS methods described herein. FIG. 10A: VH; FIG. 10B: VK; FIG. 10A: Vλ.

DETAILED DESCRIPTION OF THE INVENTION 1. Overview

As disclosed herein, conventional antibody humanization “grafts” non-human (e.g., murine) CDRs into a human framework sequence. It is generally believed that CDRs are crucial for antigen binding; therefore, the original non-human CDR sequences are maintained, and back-mutations are introduced into human framework region to restore binding affinity of the grafted CDRs. However, such humanization techniques still retain high contents of non-human amino acids. For example, one or more of the non-human residues in the CDRs may still be immunogenic in human.

Surprisingly, the inventors recognized that the six CDRs can also be mutated in ways that could not be predicted a priori. In fact, due to redundancy of amino acid usage in the antibody paratope, a significant number of CDR residues could be substituted, for example, with human germline residues to further increase the human amino acid content. For example, structural analyses illustrated that only subsets of CDR residues actually make contact with antigen. Remarkably, many CDR residues do not contact a target antigen directly; instead, these CDR residues form redundant paratope space that can be used to bind a second, unrelated antigen (Bostrom et al. Science 1610-4, 2009). This finding challenges the traditional paradigm that describes antibody-antigen interaction as a lock and key (which suggests that each antibody surface can only accommodate one antigen). If not all CDR residues are required for binding of a single antigen, then a small number of “redundant” paratope residues may be further mutated without significantly affecting binding affinities.

Accordingly, as disclosed and exemplified herein, the inventors discovered that “redundant” paratope residues in CDRs can be replaced with human germline residues to create “ultra” humanized antibodies.

For example, as shown in the examples, the inventors created several phage display libraries to screen for “ultra” humanized antibodies (with increased number of human residues in CDRs as compared to the conventional CDR grafting methods). Each library was based on a starting non-human donor antibody (rat anti-RAGE, rabbit anti-A33, and chicken anti-pTau). As illustrated in FIG. 1A, in each case, five non-human donor CDRs (CDR-L1, CDR-L2, CDR-L3, CDR-H1, and CDR-H2) were aligned with their corresponding CDRs from a human germline sequence. If a donor residue is the same as the corresponding human germline residue, that residue remained unchanged, and incorporated into all clones of the library. If a donor residue is different from the corresponding human germline residue, both residues were incorporated combinatorially into library clones.

For example, as shown in FIG. 1, the alignment of the CDR-L1 of rat anti-RAGE antibody and human germline DPK9 is as follows:

TABLE 10 Position 24 25 26 27 28 29 30 31 32 33 34 Human Germline R A S Q S I S S Y L N DPK9 SEQ ID NO: 1 Rat anti-RAGE R A S Q D V G I Y V N antibody SEQ ID NO: 2 For positions 24, 25, 26, 27, 32, and 34 (in bold), the human residue and the corresponding rat residue are the same, therefore, all library clones incorporate the same residue (e.g., “R” at position 24) at the designated position. In certain embodiments, it may be preferable to use human germline codon to encode this residue. For positions 28, 29, 30, 31, and 33, the human residue and the corresponding rat residue are different. Therefore, only a portion of the library clones comprise the human germline residue (e.g., 60% of the library clones comprise the human residue “S” at position 28), the remainder of the library clones comprise the corresponding rat residue (e.g., 40% of the library clones comprise the rat residue D at position “28”) at the designated position.

In certain embodiments, it may be desirable that for each position, about 50% of the clones have the human germline residue, and about 50% of the clones have the non-human donor residue; so that both residues are substantially equally represented in the library. However, as disclosed and exemplified herein, 50%:50% (human:non-human) distribution is not necessary. The libraries of the invention not only tolerate significant variations in human:non-human distribution, but in some circumstances, unequal distribution may be desired (e.g., to improve stability).

For CDR-H3, each position can be any one of the 20 natural amino acid residues. In certain embodiments, it may be desirable that for each position, each of the 20 natural amino acid residues are substantially equally represented in the library. Again, substantially equal distribution of the 20 natural amino acid residues is not necessary. For example, in some circumstances, the presence of certain residues may be reduced or avoided (e.g., residues that might cause stability problems).

This design principle is named “Augmented Binary Substitution” (ABS). “Binary” means that either human germline residue or non-human donor residue is used in CDR L1-L3 and H1-H2 to increase the human content of the antibody; and “augmented” refers to additional mutations introduced in CDR-H3 to further optimize the activities of the antibody.

Because both human and non-human residues are incorporated into the library clones combinatorially, it is theoretically possible that a very small number of library clones have only human germline residues in CDR-L1, CDR-L2, CDR-L3, CDR-H1 and CDR-H2 (“all human” clones). That is, each time the human and non-human donor residues differ, the human residue is incorporated, resulting in a clone that comprises the original human germline CDR-L1, CDR-L2, CDR-L3, CDR-H1 and CDR-H2 sequences. Conversely, it is also theoretically possible that a very small number of library clones have only non-human donor residues in CDR-L1, CDR-L2, CDR-L3, CDR-H1 and CDR-H2 (“all donor” clones). That is, each time human and non-human donor residues differ, the non-human donor residue is incorporated, resulting in a clone that comprises the original non-human donor CDR-L1, CDR-L2, CDR-L3, CDR-H1 and CDR-H2 sequences.

In general, all human and all donor clones should be less than 1%. Assuming that, for each antibody, there are at least seven positions (CDR-L1, CDR-L2, CDR-L3, CDR-H1 and CDR-H2 combined) where human and non-human donor residues differ, the number of “all human” library clones should be less than 1% (at least 1×2⁷, or 128 individual clones; 1 out of 128 is less than 1 percent). Similarly, the number of “all non-human” library clones should be less than 1% as well. Accordingly, more than 99% of the clones in the library should comprise at least one more human germline residue in CDR-L1, CDR-L2, CDR-L3, CDR-H1 and CDR-H2 combined as compared to the original donor CDR donor sequences; and more than 99% of the clones in the library should comprise at least one non-human donor residue in CDR-L1, CDR-L2, CDR-L3, CDR-H1 and CDR-H2 combined, as compared to the original human germline CDR sequences.

In the CDR-H3, the library may or may not need to be “Augmented” by the addition of point mutations or random mutations. “Augmentation” may encourage the “fit” for this loop either into the human v-domains or in binding to target.

Based on ABS design principle, CDR repertoires (FIG. 1) were built into human germline frameworks (DP54 and DPK9 in the Examples), then screened to identify lead clones with epitope specificity and affinity equivalent to the parental clone. This proved to be a convenient and rapid method which retains the functionally-required CDR residues of the original non-human donor antibody, without the need for prior crystal-structure insight. Notably, this CDR redundancy-minimization approach generated highly stable and soluble human IgGs, from multiple key antibody discovery species. The resulting antibodies have significantly reduced non-human residue content, such as t-cell epitope content (which is a major risk factor for antibody immunogenicity in human) and reduced non-human germline surface amino acid exposure, which may lead to reduced B-cell epitope content.

2. Definitions

An antibody “variable domain” refers to the variable region of the antibody light chain (VL) or the variable region of the antibody heavy chain (VH), either alone or in combination. As known in the art, the variable regions of the heavy and light chains each consist of four framework regions (FR) connected by three complementarity determining regions (CDRs), and contribute to the formation of the antigen binding site of antibodies.

Residues in a variable domain are numbered according Kabat, which is a numbering system used for heavy chain variable domains or light chain variable domains of the compilation of antibodies. See, Kabat et al., Sequences of Proteins of Immunological Interest, 5th Ed. Public Health Service, National Institutes of Health, Bethesda, Md. (1991)). Using this numbering system, the actual linear amino acid sequence may contain fewer or additional amino acids corresponding to a shortening of, or insertion into, a FR or CDR of the variable domain. For example, a heavy chain variable domain may include a single amino acid insert (residue 52a according to Kabat) after residue 52 of H2 and inserted residues (e.g. residues 82a, 82b, and 82c, etc according to Kabat) after heavy chain FR residue 82. The Kabat numbering of residues may be determined for a given antibody by alignment at regions of homology of the sequence of the antibody with a “standard” Kabat numbered sequence.

Various algorithms for assigning Kabat numbering are available. The algorithm implemented in the 2012 release of Abysis (www.abysis.org) is used herein to assign Kabat numbering to variable regions unless otherwise noted.

The term “Complementarity Determining Regions” (CDRs) are defined as follows (numbering according to Kabat; H: heavy chain; L: light chain):

-   -   CDR-HI: H26-H35B; CDR-H2: H49-H65; CDR-H3: H95-H102     -   CDR-LI: L24-L34; CDR-L2: L50-L56; CDR-L3: L89-L97         The boundaries of the CDRs defined herein are not identical to         the CDRs originally defined by Kabat (1991), and the definition         of instant disclosure controls.

“Framework” (FR) residues are antibody variable domain residues other than the CDR residues. A VH or VL domain framework comprises four framework sub-regions, FR1, FR2, FR3 and FR4, interspersed with CDRs in the following structure: FR1-CDR1-FR2-CDR2-FR3-CDR3-FR4. According to the definition provided herein, FR residues include the following (number according to Kabat; H: heavy chain; L: light chain):

TABLE 11 FR1 FR2 FR3 FR4 Heavy Chain H1-H25 H36-H48 H66-H94 H103-H113 Light Chain L1-L23 L35-L49 L57-L88 L98-L107

An “antigen-binding fragment” of an antibody refers to a fragment of a full-length antibody that retains the ability to specifically bind to an antigen (preferably with substantially the same binding affinity). Examples of an antigen-binding fragment includes (i) a Fab fragment, a monovalent fragment consisting of the VL, VH, CL and CH1 domains; (ii) a F(ab′)2 fragment, a bivalent fragment comprising two Fab fragments linked by a disulfide bridge at the hinge region; (iii) a Fd fragment consisting of the VH and CH1 domains; (iv) a Fv fragment consisting of the VL and VH domains of a single arm of an antibody, (v) a dAb fragment (Ward et al., (1989) Nature 341:544-546), which consists of a VH domain; and (vi) an isolated complementarity determining region (CDR), disulfide-linked Fvs (dsFv), and anti-idiotypic (anti-Id) antibodies and intrabodies. Furthermore, although the two domains of the Fv fragment, VL and VH, are coded for by separate genes, they can be joined, using recombinant methods, by a synthetic linker that enables them to be made as a single protein chain in which the VL and VH regions pair to form monovalent molecules (known as single chain Fv (scFv)); see e.g., Bird et. al. Science 242:423-426 (1988) and Huston et al. Proc. Natl. Acad. Sci. USA 85:5879-5883 (1988)). Other forms of single chain antibodies, such as diabodies are also encompassed. Diabodies are bivalent, bispecific antibodies in which VH and VL domains are expressed on a single polypeptide chain, but using a linker that is too short to allow for pairing between the two domains on the same chain, thereby forcing the domains to pair with complementary domains of another chain and creating two antigen binding sites (see e.g., Holliger et al. Proc. Natl. Acad. Sci. USA 90:6444-6448 (1993); Poljak et al., 1994, Structure 2:1121-1123).

A “human antibody” is an antibody comprising an amino acid sequence that is derived from a human germline, such as an antibody expressed by a human B cell, or an antibody expressed by a transgenic animal that comprises a nucleic acid sequence encoding a human immunoglobulin. Also included herein is an antibody that comprises a consensus human antibody sequence. For example, the framework sequence of a human antibody can be a specific human germline framework sequence (e.g., Tables 2-4), or a consensus human germline framework sequence (e.g., Tables 5-6). This definition of a human antibody specifically excludes a humanized antibody comprising non-human CDR sequences.

A “non-human donor antibody” includes any antibody that is not a “human antibody” defined herein. A non-human donor antibody can be an antibody comprising an amino acid sequence that corresponds to an immunoglobulin produced by non-human species. The CDR residues (and a selected number of framework residues) of a non-human antibody can be used as “donor” residues during humanization process. Also included herein is a CDR-grafted antibody in which CDR sequences from a non-human species (such as murine) are grafted into a human framework. One aspect of the invention is to further humanize CDR-grafted, humanized antibody, by introducing additional human germline residues in the CDR region. Therefore, a CDR-grafted, humanized antibody can also serve as a “non-human donor” antibody.

“Corresponding” CDR or FR residues from different antibodies can be identified according to sequence alignment or structural alignment that is known in the art. For example, “corresponding” CDR or FR residues from different antibodies can be identified by alignment according to Kabat numbering, or any other numbering systems that are known in the art, such as AHo, IMGT, Chothia, or AbM. “Corresponding” CDR or FR residues share the same numbers under such a numbering system. Alternatively, alignments can be done by hand or by using well-known sequence alignment programs such as ClustalW2, or “BLAST 2 Sequences” using default parameters. For example, NCBI “IgBLAST” is specifically for antibodies.

In addition to sequence alignment, structural alignment may also be used to identify “corresponding” CDR or FR residues. Structural alignments use information about the secondary and tertiary structure to aid in aligning the sequences. These methods are used for two or more sequences and typically produce local alignments; however, because they depend on the availability of structural information, they can only be used for sequences whose corresponding structures are known (usually through X-ray crystallography or NMR spectroscopy). Sometimes, structural alignments can be more reliable between sequences that are very distantly related and that have diverged so extensively that sequence comparison cannot reliably detect their similarity. Where there is no available structural data on one of the proteins, a comparison can still be made if structural data is available on one or preferably more closely related proteins, such as immunoglobulins across species, and in particular antibody constant domains across species and subtype. A commonly used algorithm for structural alignments is TM-ALIGN (Zhang and Skolnick, Nucleic Acids Research, 33: 2302-2309 (2005)), which assigns increased weight to the most similar regions of the structure during superposition.

In certain embodiments, one or more “back-mutations” may be used during CDR grafting. A back-mutation refers to a mutation in antibody variable domain framework region where a human germline residue is replaced with the corresponding non-human donor residue to increase the antigen binding affinity of a humanized antibody. A “random mutation” refers to the substitution of an amino acid residue with a different amino acid residue.

Specific amino acid residue positions are also numbered according to Kabat. For example, for human VK1 germline IGKV1-39 used in the examples, “Leu46” (or L46) refers to position 46 according to Kabat numbering (which is a Leu). However, the “Leu46” (or L46) designation includes any residue from another antibody (e.g., an antibody from another human or non-human antibody) that corresponds to Leu46 of human VK1 germline IGKV1-39 (even though the actual position of that residue may or may not be 46, and the actual residue may or may not be Leu). For example, for human VK1D germline IGKV1D-16, position 46 (Kabat numbering) is Ser, and VK1D germline IGKV1 D-17, position 46 (Kabat numbering) is His. Therefore, for simplicity, Leu46 (or L46) is used to refer a residue that aligns with Leu46 of IGKV1-39, even if it is a Ser or His. Similarly, mutations are also identified according to Kabat numbering. For example, Leu46Thr (or “L46T”) means that a residue from an antibody that corresponds to Leu46 of human germline IGKV1-39 (which may or may not be Leu) is mutated to Thr.

The binding affinity of an antibody can be expressed as Kd value, which refers to the dissociation rate of a particular antigen-antibody interaction. Kd is the ratio of the rate of dissociation, also called the “off-rate (koff)”, to the association rate, or “on-rate (kon)”. Thus, Kd equals koff/kon and is expressed as a molar concentration (M), and the smaller the Kd, the stronger the affinity of binding. Kd values for antibodies can be determined using methods well established in the art. One exemplary method for measuring Kd is surface plasmon resonance (SPR), typically using a biosensor system such as a BIACORE® system. BIAcore kinetic analysis comprises analyzing the binding and dissociation of an antigen from chips with immobilized molecules (e.g. molecules comprising epitope binding domains), on their surface. Another method for determining the Kd of an antibody is by using Bio-Layer Interferometry, typically using OCTET® technology (Octet QKe system, ForteBio). For example, a standard assay condition for surface plasmon resonance can be based on ligand immobilization of approximately 100 Response Units (RU) of IgG on the SPR chip. Purified target proteins are diluted in buffer to a range of final concentrations and injected at a requisite flow rate (e.g. 10-100 μl/min) to allow the calculation of K_(a). Dissociation is allowed to proceed to establish off-rate (K_(d)), followed by a 5 sec pulse of 20 mM NaOH for regeneration of the chip surface. Sensorgrams are then analyzed using a kinetics evaluation software package.

The term “about”, as used here, refers to +/−10% of a value.

3. Humanized Antibodies and Antibody Libraries

Provided herein are libraries for humanizing a non-human donor antibody that binds to a target antigen, wherein: (a) said library comprises a plurality of polypeptides, each polypeptide comprising an antibody variable domain; (b) said antibody variable domain comprises (i) a VH domain comprising: a human germline VH framework sequence, and CDR-H1, CDR-H2, and CDR-H3; and (ii) a VL domain comprising: a human germline VL framework sequence, and CDR-L1, CDR-L2, and CDR-L3; (c) for each individual position within said CDR-L1, CDR-L2, CDR-L3, CDR-H1, and CDR-H2: if the human germline residue at said position is the same as the corresponding non-human donor residue, all polypeptides in the library comprise the human germline residue at said position; if the human germline residue at the position is different from the corresponding non-human donor residue, a portion of the polypeptides in the library comprise the human germline residue at said position, the remainder of the polypeptides comprise the corresponding non-human donor residue at said position; (d) for each individual position within CDR-H3, the residue is any one of the 20 natural amino acid residues. In addition, less than 1% of the polypeptides in said library comprise the original non-human donor CDR-L1, CDR-L2, CDR-L3, CDR-H1, and CDR-H2 sequences; and less than 1% of the polypeptides in said library comprise the original human VL germline CDR-L1, CDR-L2, and CDR-L3, and the original human VH germline CDR-H1 and CDR-H2 sequences.

The libraries disclosed herein can be used to screen for “ultra” humanized antibodies, in particular antibodies where human germline residues are incorporated into non-human donor CDRs. Accordingly, also provided herein is humanized antibody or antigen-binding fragment thereof that binds to a target antigen, wherein: (a) said antibody or antigen-binding fragment thereof comprises (i) a VH domain comprising: a human germline VH framework sequence, and CDR-H1, CDR-H2, and CDR-H3; and (ii) a VL domain comprising: a human germline VL framework sequence, and CDR-L1, CDR-L2, and CDR-L3; (b) said CDR-L1, CDR-L2, CDR-L3, CDR-H1, and CDR-H2 are derived from corresponding CDRs from a non-human donor antibody that binds to said target antigen; (c) for each position within said CDR-L1, CDR-L2, CDR-L3, CDR-H1, and CDR-H2, the residue is either human germline residue from said human germline VL or VH, or corresponding residue from said non-human donor antibody; (d) said CDR-L1, CDR-L2, CDR-L3, CDR-H1, and CDR-H2 each comprises at least one more human germline residue as compared to the corresponding non-human donor CDR, (e) said CDR-L1, CDR-L2, CDR-L3, CDR-H1, and CDR-H2 each comprises at least one more non-human donor residue as compared to the corresponding human germline VH or VL CDR; and (f) for each position within CDR-H3, the residue is any one of the 20 natural amino acid residues.

A. Non-human Donor Antibodies

Humanization generally starts with obtaining CDR sequences from a non-human donor antibody that binds to a target antigen, and incorporating non-human donor residues into a human framework.

Non-human donor antibody binds to a target antigen and can be obtained, e.g., by conventional techniques (such as hybridoma technology, recombinant DNA technology). For example, the target antigen may be isolated from a natural source, or may be produced recombinantly or by in vitro synthesis. Alternatively, cells comprising native or recombinant antigen can be used. The antigen can be administered to a suitable non-human host to induce production of antibodies. Monoclonal antibodies can then be obtained by, for example, hybridoma technology.

Multiple non-human donor antibodies can be screened to select an antibody that has strong binding affinity for the target antigen. For example, the non-human donor antibody may bind the antigen of interest with a binding affinity (Kd) value of about 1×10⁻⁵ M or less, such as about 1×10⁻⁵ M or less, about 1×10⁻⁶ M or less, about 1×10⁻⁷ M or less, about 1×10⁻⁸ M or less, about 1×10⁻⁹ M or less, about 1×10⁻¹⁰ M or less, about 1×10⁻¹ M or less, about 1×10⁻¹² M or less, about 1×10⁻¹³ M or less, from about 1×10⁻⁵ M to about 1×10⁻¹³ M, from about 1×10⁻⁶ M to about 1×10⁻¹³ M, from about 1×10⁻⁷ M to about 1×10⁻¹³ M, from about 1×10⁻⁸ M to about 1×10⁻¹³ M, from about 1×10⁻⁹ M to about 1×10⁻¹³ M, from about 1×10⁻⁵ M to about 1×10⁻¹² M, from about 1×10⁻⁶ M to about 1×10⁻¹² M, from about 1×10⁻⁷ M to about 1×10⁻¹² M, from about 1×10⁻⁸ M to about 1×10⁻¹² M, from about 1×10⁻⁹ M to about 1×10⁻¹² M, from about 1×10⁻⁵ M to about 1×10¹¹ M, from about 1×10⁻⁶ M to about 1×10¹¹ M, from about 1×10⁻⁷ M to about 1×10¹¹ M, from about 1×10⁻⁸ M to about 1×10¹¹ M, or from about 1×10⁻⁹ M to about 1×10¹¹ M. Generally, the antibody will bind antigen with an affinity in the nanomolar or better range.

The sequence of the non-human donor antibody can be determined using standard sequencing techniques, or obtained from a sequence database or other literature resources. If desired, polynucleotide sequence(s) encoding the antibody may then be cloned into a vector for expression or propagation.

The CDR and framework sequences of the non-human donor antibody can be readily ascertained using standard antibody numbering systems, such as Kabat numbering.

Examples of antigens include: HER2, CD20, TNF ALPHA, C5, C5a, CD30, Blys, CTLA-4, IL1B, PD-1, PDL-1, IL12, IL23, IL17a, VEGF, EGFR, IL-6R, CD11a, APLHA-4-INTEGRIN, IgE, CD52, CD33, CD25, RSV, B. anthracis protective antigen, CD3, IL33, P-CADHERIN, NOTCH1, EPHA4, 5T4, IL4, IL13, MADCAM, IL6, 41BB, OX-40, TFPI, CXCR4, and FGF21.

Additional examples of antigens include: PDGFRα, PDGFRβ, PDGF, VEGF, VEGF-A, VEGF-B, VEGF-C, VEGF-D, VEGF-E, VEGF-F, VEGFR1, VEGFR2, VEGFR3, FGF, FGF2, HGF, KDR, fit-1, FLK-1, Ang-2, Ang-1, PLGF, CEA, CXCL13, Baff, IL-21, CCL21, TNF-α, CXCL12, SDF-I, bFGF, MAC-I, IL23pl9, FPR, IGFBP4, CXCR3, TLR4, CXCR2, EphA2, EphA4, EphrinB2, EGFR(ErbB1), HER2(ErbB2 or p185neu), HER3(ErbB3), HER4 ErbB4 or tyro2), SCI, LRP5, LRP6, RAGE, s100A8, s100A9, Navl.7, GLPI, RSV, RSV F protein, Influenza HA protein, Influenza NA protein, HMGBI, CD16, CD19, CD20, CD21, CD28, CD32, CD32b, CD64, CD79, CD22, ICAM-I, FGFRI, FGFR2, HDGF, EphB4, GITR, β-amyloid, hMPV, PIV-I, PIV-2, OX40L, IGFBP3, cMet, PD-I, PLGF, Neprolysin, CTD, IL-18, IL-6, CXCL-13, IL-IRI, IL-15, IL-4R, IgE, PAI-I, NGF, EphA2, uPARt, DLL-4, αvβ5, αvβ6, α5β1, α3β1, interferon receptor type I and type II, CD 19, ICOS, IL-17, Factor II, Hsp90, IGF, IGF-I, IGF-II, CD 19, GM-CSFR, PIV-3, CMV, IL-13, IL-9, and EBV.

Additional examples of antigens include: Tumor Necrosis Factor-α (“TNF-α”), Tumor Necrosis Factor-β (“TNF-β”), Lymphotoxin-α (“LT-α”), CD30 ligand, CD27 ligand, CD40 ligand, 4-1 BB ligand, Apo-1 ligand (also referred to as Fas ligand or CD95 ligand), Apo-2 ligand (also referred to as TRAIL), Apo-3 ligand (also referred to as TWEAK), osteoprotegerin (OPG), APRIL, RANK ligand (also referred to as TRANCE), TALL-I (also referred to as BlyS, BAFF or THANK), DR4, DR5 (also known as Apo-2, TRAIL-R2, TR6, Tango-63, hAPO8, TRICK2, or KILLER), DR6, DcRI, DcR2, DcR3 (also known as TR6 or M68), CARI, HVEM (also known as ATAR or TR2), GITR, ZTNFR-5, NTR-I, TNFLI, CD30, LTBr, 4-1BB receptor and TR9.

Additional examples of antigens include: 5T4, ABL, ABCB5, ABCFI, ACVRI, ACVRIB, ACVR2, ACVR2B, ACVRLI, ADORA2A, Aggrecan, AGR2, AICDA, AIFI, AIGI, AKAPI, AKAP2, AMH, AMHR2, angiogenin (ANG), ANGPTI, ANGPT2, ANGPTL3, ANGPTL4, Annexin A2, ANPEP, APC, APOCI, AR, aromatase, ATX, AXI, AZGPI (zinc-a-glycoprotein), B7.1, B7.2, B7-H1, BAD, BAFF, BAGI, BAII, BCR, BCL2, BCL6, BDNF, BLNK, BLRI (MDR15), BlyS, BMP1, BMP2, BMP3B (GDFIO), BMP4, BMP6, BMP7, BMP8, BMP9, BMP11, BMP12, BMPR1A, BMPR1B, BMPR2, BPAGI (plectin), BRCAI, C19orflO (IL27w), C3, C4A, C5, C5R1, CANTI, CASPI, CASP4, CAVI, CCBP2 (D6/JAB61), CCLI (1-309), CCLI 1 (eotaxin), CCL13 (MCP-4), CCL15 (MIP-Id), CCL16 (HCC-4), CCL17 (TARC), CCL18 (PARC), CCL19 (MIP-3b), CCL2 (MCP-1), MCAF, CCL20 (MIP-3a), CCL21 (MEP-2), SLC, exodus-2, CCL22(MDC/STC-I), CCL23 (MPIF-I), CCL24 (MPIF-2/eotaxin-2), CCL25 (TECK), CCL26(eotaxin-3), CCL27 (CTACK/ILC), CCL28, CCL3 (MIP-Ia), CCL4 (MIP-Ib), CCL5(RANTES), CCL7 (MCP-3), CCL8 (mcp-2), CCNAI, CCNA2, CCNDI, CCNEI, CCNE2, CCRI (CKRI/HM145), CCR2 (mcp-IRB/RA),CCR3 (CKR3/CMKBR3), CCR4, CCR5(CMKBR5/ChemR13), CCR6 (CMKBR6/CKR-L3/STRL22/DRY6), CCR7 (CKR7/EBI1),CCR8 (CMKBR8/TERI/CKR-LI), CCR9 (GPR-9-6), CCRLI (VSHKI), CCRL2 (L-CCR),CD164, CD19, CDIC, CD20, CD200, CD-22, CD24, CD28, CD3, CD33, CD35, CD37, CD38, CD3E, CD3G, CD3Z, CD4, CD40, CD40L, CD44, CD45RB, CD46, CD52, CD69, CD72, CD74, CD79A, CD79B, CD8, CD80, CD81, CD83, CD86, CD105, CD137, CDHI (E-cadherin), CDCP1CDH10, CDH12, CDH13, CDH18,CDH19, CDH20, CDH5, CDH7, CDH8, CDH9, CDK2, CDK3, CDK4, CDK5, CDK6, CDK7, CDK9, CDKNIA (p21WapI/CipI), CDKNIB (p27KipI), CDKNIC, CDKN2A (pl61INK4a), CDKN2B, CDKN2C, CDKN3, CEBPB, CERI, CHGA, CHGB, Chitinase, CHSTIO, CKLFSF2, CKLFSF3, CKLFSF4, CKLFSF5, CKLFSF6, CKLFSF7, CKLFSF8, CLDN3, CLDN7 (claudin-7), CLN3, CLU (clusterin), CMKLRI, CMKORI (RDCI), CNRI, COLI 8AI, COL1A1.COL4A3, COL6A1, CR2, Cripto, CRP, CSFI (M-CSF), CSF2 (GM-CSF), CSF3 (GCSF), CTLA4, CTL8, CTNNBI (b-catenin), CTSB (cathepsin B), CX3CL1 (SCYDI), CX3CR1 (V28), CXCLI(GROI), CXCLIO (IP-IO), CXCLII (I-TAC/IP-9), CXCL12 (SDFI), CXCL13, CXCL 14,CXCL 16, CXCL2 (GR02), CXCL3 (GR03), CXCL5 (ENA-78/LIX), CXCL6 (GCP-2), CXCL9 (MIG), CXCR3 (GPR9/CKR-L2), CXCR4, CXCR6 (TYMSTR/STRL33/Bonzo), CYB5, CYCI, Cyr61, CYSLTRI, c-Met, DAB21P, DES, DKFZp451J0118, DNCLI, DPP4, E2F1, ECGFI5EDGI, EFNAI, EFNA3, EFNB2, EGF, ELAC2, ENG, endoglin, ENOI, EN02, EN03, EPHAI, EPHA2, EPHA3, EPHA4, EPHA5, EPHA6, EPHA7, EPHA8, EPHA9, EPHAIO, EPHBI, EPHB2, EPHB3, EPHB4, EPHB5, EPHB6, EPHRIN-AI, EPHRIN-A2, EPHRIN-A3, EPHRIN-A4, EPHRIN-A5, EPHRIN-A6, EPHRIN-BI, EPHRIN-B2, EPHRTN-B3, EPHB4,EPG, ERBB2 (Her-2), EREG, ERK8, Estrogen receptor, ESRI, ESR2, F3 (TF), FADD, farnesyltransferase, FasL, FASNf, FCER1A,FCER2, FCGR3A, FGF, FGFI (aFGF), FGFIO, FGFI 1, FGF12, FGF12B, FGF13, FGF14, FGF16, FGF17, FGF18, FGF19, FGF2 (bFGF), FGF20, FGF21 (such as mimAb1), FGF22, FGF23, FGF3 (int-2), FGF4 (HST), FGF5, FGF6 (HST-2), FGF7 (KGF), FGF8, FGF9, FGFR3, FIGF (VEGFD), FILI(EPSILON), FBLI (ZETA), FLJ12584, FLJ25530, FLRTI (fibronectin), FLTI, FLT-3, FOS, FOSLI(FRA-I), FY (DARC), GABRP (GABAa), GAGEBI, GAGECI, GALNAC4S-6ST, GATA3, GD2, GD3, GDF5, GDF8, GFII, GGTI, GM-CSF, GNASI, GNRHI, GPR2 (CCRIO), GPR31, GPR44, GPR81 (FKSG80), GRCCIO (CIO), gremlin, GRP, GSN (Gelsolin), GSTPI, HAVCR2, HDAC, HDAC4, HDACS5, HDAC7A, HDAC9, Hedgehog, HGF, HIFIA, HIPI, histamine and histamine receptors, HLA-A, HLA-DRA, HM74, HMOXI, HSP90, HUMCYT2A, ICEBERG, ICOSL, ID2, IFN-α, IFNAI, IFNA2, IFNA4,1FNA5, EFNA6, BFNA7, IFNBI, IFNgamma, IFNWI, IGBPI, IGFI, IGFIR, IGF2, IGFBP2,IGFBP3, IGFBP6, DL-I, ILIO, ILIORA, ILIORB, IL-1, ILIRI (CD121a), ILIR2(CD121b), IL-IRA, IL-2, IL2RA (CD25), IL2RB(CD122), IL2RG(CD132), IL-4, IL-4R(CD123), IL-5, IL5RA(CD125), IL3RB(CD131), IL-6, IL6RA (CD126), IR6RB(CD130), IL-7, IL7RA(CD127), IL-8, CXCRI (IL8RA), CXCR2 (IL8RB/CD128), IL-9, IL9R (CD129), IL-10, IL10RA(CD210), IL10RB(CDW210B), IL-11, IL1IRA, IL-12, IL-12A, IL-12B, IL-12RB1, IL-12RB2, IL-13, IL13RA1, IL13RA2, IL14, IL15, IL15RA, 1L16, IL17, IL17A, IL17B, IL17C, IL17R, IL18, IL18BP, IL18R1, IL18RAP, IL19, ILIA, ILIB, ILIFIO, IL1F5, IL1F6, IL1F7, IL1F8, DL1F9, ILIHYI, ILIRI, IL1R2, ILIRAP, ILIRAPLI, IL1 RAPL2, ILIRLI, IL1RL2, ILIRN, IL2, IL20, IL20RA, IL21R, IL22, IL22R, IL22RA2, IL23,DL24, IL25, IL26, IL27, IL28A, IL28B, IL29, IL2RA, IL2RB, IL2RG, IL3, IL30, IL3RA, IL4,IL4R, IL6ST (glycoprotein 130), ILK, INHA, INHBA, INSL3, INSL4, IRAKI, IRAK2, ITGA1, ITGA2, ITGA3, ITGA6 (α 6 integrin), ITGAV, ITGB3, ITGB4 (β 4 integrin), JAKI, JAK3, JTB, JUN, K6HF, KAII, KDR, KIM-1, KITLG, KLF5 (GC Box BP), KLF6, KLKIO, KLK12, KLK13, KLK14, KLK15, KLK3, KLK4, KLK5, KLK6, KLK9, KRTI, KRT19 (Keratin 19), KRT2A, KRTHB6 (hair-specific type II keratin), LAMA5, LEP (leptin), Lingo-p75, Lingo-Troy, LPS, LRP5, LRP6, LTA (TNF-b), LTB, LTB4R (GPR16), LTB4R2, LTBR, MACMARCKS, MAG or Omgp, MAP2K7 (c-Jun), MCP-I, MDK, MIBI, midkine, MIF, MISRII, MJP-2, MK, MKI67 (Ki-67), MMP2, MMP9, MS4A1, MSMB, MT3 (metallothionectin-Ui), mTOR, MTSSI, MUCI (mucin), MYC, MYD88, NCK2, neurocan, neuregulin-1, neuropilin-1, NFKBI, NFKB2, NGFB (NGF), NGFR, NgR-Lingo, NgR-Nogo66 (Nogo), NgR-p75, NgR-Troy, NMEI (NM23A), NOTCH, NOTCHI, N0X5, NPPB, NROBI, NR0B2, NRIDI, NR1D2, NR1H2, NR1H3, NR1H4, NR1I2, NR1I3, NR2C1, NR2C2, NR2E1, NR2E3, NR2F1, NR2F2, NR2F6, NR3C1, NR3C2, NR4A1, NR4A2, NR4A3, NR5A1, NR5A2, NR6A1, NRPI, NRP2, NT5E, NTN4, OCT-1, ODZ1, OPN1, OPN2, OPRDI, P2RX7, PAP, PARTI, PATE, PAWR, PCA3, PCDGF, PCNA, PDGFA, PDGFB, PDGFRA, PDGFRB, PECAMI, peg-asparaginase, PF4 (CXCL4), Plexin B2 (PLXNB2), PGF, PGR, phosphacan, PIAS2, PI3 Kinase, PIK3CG, PLAU (uPA), PLG5PLXDCI, PKC, PKC-β, PPBP (CXCL7), PPID, PRI, PRKCQ, PRKDI, PRL, PROC, PROK2, pro-NGF, prosaposin, PSAP, PSCA, PTAFR, PTEN, PTGS2 (COX-2), PTN, RAC2 (P21Rac2), RANK, RANK ligand, RARB, RGSI, RGS13, RGS3, RNFI10 (ZNF144), Ron, ROB02, RXR, selectin, S100A2, S100A8, S100A9, SCGB 1D2 (lipophilin B), SCGB2A1 (mammaglobin 2),SCGB2A2 (mammaglobin 1), SCYEI (endothelial Monocyte-activating cytokine), SDF2, SERPENA1, SERPINA3, SERPINB5 (maspin), SERPINEI (PAI-I), SERPINFI, SHIP-I, SHIP-2, SHBI, SHB2, SHBG, SfcAZ, SLC2A2, SLC33A1, SLC43A1, SLIT2, SPPI, SPRRIB (SprI), ST6GAL1, STABI, STAT6, STEAP, STEAP2, SULF-1, Sulf-2, TB4R2, TBX21, TCPIO, TDGFI, TEK, TGFA, TGFBI, TGFBIII, TGFB2,TGFB3, TGFBI, TGFBRI, TGFBR2, TGFBR3, THIL, THBSI (thrombospondin-1), THBS2/THBS4, THPO, TIE (Tie-1), TIMP3, tissue factor, TIKI2, TLR10, TLR2, TLR3, TLR4, TLR5, TLR6JLR7, TLR8, TLR9, TM4SF1, TNF, TNF-α, TNFAIP2 (B94), TNFAIP3, TNFRSFIIA, TNFRSFIA, TNFRSFIB, TNFRSF21, TNFRSF5, TNFRSF6 (Fas), TNFRSF7, TNFRSF8, TNFRSF9, TNFSFIO (TRAIL), TNFSFI 1 (TRANCE), TNFSF12 (AP03L), TNFSF13 (April), TNFSF13B, TNFSF14 (HVEM-L), TNFSF15 (VEGI), TNFSF 18, TNFSF4 (OX40 ligand), TNFSF5 (CD40 ligand), TNFSF6 (FasL), TNFSF7 (CD27 ligand), TNFSF8 (CD30 ligand), TNFSF9 (4-1BB ligand), TOLLIP, Toll-like receptors, TLR2, TLR4, TLR9, TOP2A (topoisomerase lia), TP53, TPMI, TPM2,TRADD, TRAFI, TRAF2, TRAF3, TRAF4, TRAF5, TRAF6, TRKA, TREMI, TREM2, TRPC6, TROY, TSLP, TWEAK, Tyrosinase, uPAR, VEGF, VEGFB, VEGFC, versican, VHL C5, VLA-4, Wnt-1, XCLI (lymphotactin), XCL2 (SCM-Ib), XCRI (GPR5/CCXCRI), YYI, and ZFPM2.

Examples of non-human donor antibodies can be a non-human mammalian antibody (e.g., murine antibody, a rat antibody, a rabbit antibody, a llama antibody, an alpaca antibody), or an avian antibody (e.g., a chicken antibody or from any domesticated or non-domesticated bird). A camelid VHH single domain antibody (llama, alpaca or dromedary) may also be used. A CDR-grafted, humanized antibodies can also be used as a donor, to further humanize such antibodies by introducing additional human germline residues in the CDR region.

B. Human Frameworks

Sequences of human germline frameworks are available from various public databases, such as V-base, IMGT, NCBI, or Abysis. Exemplary human framework sequences are listed in Tables 2-6.

Suitable human framework can be the framework region from a particular human germline (Tables 2-4), or can be framework region of consensus germline sequences (Tables 5, 6).

Preferred human germline heavy chain frameworks are frameworks derived from VH1, VH3, or VH5 germlines. For example, VH frameworks from the following germlines may be used: IGHV3-23, IGHV3-7, or IGHV1-69 (germline names are based on IMGT germline definition).

Preferred human germline light chain frameworks are frameworks derived from V_(K) or V_(λ) germlines. For example, VL frameworks from the following germlines may be used: IGKV1-39 or IGKV3-20 (germline names are based on IMGT germline definition).

One exemplary method of selecting a suitable human framework is based sequence homology between non-human donor framework sequence and human framework sequences. For example, one can align the non-human donor framework sequence with various human framework sequences, and select the most homologous framework sequence. Alternatively, one may also select a framework on the basis of structural complimentarity (e.g., similarity in canonical CDR structure and therefore CDR presentation complimentarity).

As exemplified herein, in many cases, back-mutations in framework region (where a human germline residue is replaced with the corresponding non-human donor residue to restore binding affinity) is not required for the ABS method. For example, when the donor CDRs are from a mammalian species, high affinity humanized antibody were obtained without framework back-mutations (see Examples section). When the donor CDRs are from an avian species, only one back-mutation was made (see Examples section).

Accordingly, when the donor CDRs are from a mammalian species, in certain embodiment, the human germline VL framework comprises no more than 5 back-mutations or random mutations (such as 5, 4, 3, 2, or 1 back-mutation or random mutation); in certain embodiments, the human germline VH framework comprises no more than 5 back-mutations or random mutations (such as 5, 4, 3, 2, or 1 back-mutations or random mutation); in certain embodiments, the human germline VL framework and VH framework together comprise no more than 5 back-mutations or random mutations (such as 5, 4, 3, 2, or 1 back-mutation or random mutation); in certain embodiments, the human germline VL framework and VH framework together does not comprise a back-mutation or random mutation.

In particular, 1 or more back-mutations or random mutations can occur in heavy chain FR3, at positions H71-H80. Structural studies show that residues H71-H80 form a loop and play an auxiliary role for antigen binding in many natural antibodies. Some even refer to this region as “CDR4.” The structure-based database indicates that this region can accommodate diversities comparable to those observed in the classical CDRs. Further, there appears to be no significant structural constraint on the diversity within the central portion of the loop. Accordingly, if desired, positions H71-H80 (in FR3) of heavy chain can be further mutated. In certain embodiment, positions H71-H80 (in FR3) of heavy chain are constructed in binary substitution form—each position is human germline residue or corresponding non-human donor residue, in a fashion similar to that of CDR-L1, CDR-L2, CDR-L3, CDR-H1, and CDR-H2. In certain embodiment, positions H71-H80 (in FR3) of heavy chain are randomized—each position within H71-H80 can be any one of the 20 natural amino acids, in a fashion similar to that of CDR-H3.

When the donor CDRs are from an avian species, in certain embodiment, the human germline VL framework comprises no more than 10 back-mutations or random mutations (such as 10, 9, 8, 7, 6, 5, 4, 3, 2, or 1 back-mutation or random mutation); in certain embodiments, the human germline VH framework comprises no more than 10 back-mutations or random mutations (such as 10, 9, 8, 7, 6, 5, 4, 3, 2, or 1 back-mutation or random mutation); in certain embodiments, the human germline VL framework and VH framework together comprise no more than 10 back-mutations or random mutations (such as 10, 9, 8, 7, 6, 5, 4, 3, 2, or 1 back-mutation or random); in certain embodiments, the human germline VL framework and VH framework together comprise a single back-mutation or random mutation.

In an exemplary embodiment, the human germline VL framework comprises a back-mutation at position 46.

In an exemplary embodiment, the non-human CDRs are from a chicken antibody, and the back-mutation is at Leu46Thr (L46T).

As described above, 1 or more back-mutations or random mutations can occur in heavy chain FR3, at positions H71-H80.

C. Humanization of Donor CDRs

The ABS method disclosed herein modifies the donor CDR residues to increase the human content of donor CDRs.

As illustrated in FIG. 1A, five non-human donor CDRs (CDR-L1, CDR-L2, CDR-L3, CDR-H1, and CDR-H2) are aligned with their corresponding CDRs from a human germline sequence. If a donor residue is the same as the corresponding human germline residue, that residue remained unchanged, and all library clones incorporate this residue at the designated position. If a donor residue is different from the corresponding human germline residue, both residues are incorporated combinatorially into library clones (i.e., a portion of the polypeptides in the library comprise the human germline residue at the designated position, the remainder of the polypeptides comprise the corresponding non-human donor residue at the designated position.

In certain embodiments, it may be desirable that for each position, about 50% of the clones had the human germline residue, and about 50% of the clones have the non-human donor residue; so that both residues are substantially equally represented in the library. However, it should be understood that even if the synthesis scheme is carried out to achieve the goal of 50%/50% for human/non-human distribution, certain synthesis biases may exist, and substantially equal distribution may not be achieved. For example, experimental and/or mechanical error in the synthesis methods used to generate DNA libraries may lead to the imprecise incorporation of individual nucleotides or codons such that 50:50 distribution of human to non-human is not achieved. In fact, in many cases, substantially equal distribution of human/non-human residues is also not necessary.

Accordingly, in certain embodiments, for each position within CDR-L1, CDR-L2, CDR-L3, CDR-H1, and CDR-H2, the percentage of polypeptides in the library comprising the human germline residue can be from about 1% to about 99%, such as from about 5% to about 95%, from about 10% to about 95%, from about 15% to about 95%, from about 20% to about 95%, from about 25% to about 95%, from about 30% to about 95%, from about 35% to about 95%, from about 40% to about 95%, from about 5% to about 90%, from about 10% to about 90%, from about 15% to about 90%, from about 20% to about 90%, from about 25% to about 90%, from about 30% to about 90%, from about 35% to about 90%, from about 40% to about 90%, from about 5% to about 85%, from about 10% to about 85%, from about 15% to about 85%, from about 20% to about 85%, from about 25% to about 85%, from about 30% to about 85%, from about 35% to about 85%, from about 40% to about 85%, from about 5% to about 80%, from about 10% to about 80%, from about 15% to about 80%, from about 20% to about 80%, from about 25% to about 80%, from about 30% to about 80%, from about 35% to about 80%, from about 40% to about 80%, from about 5% to about 75%, from about 10% to about 75%, from about 15% to about 75%, from about 20% to about 75%, from about 25% to about 75%, from about 30% to about 75%, from about 35% to about 75%, from about 40% to about 75%, from about 5% to about 70%, from about 10% to about 70%, from about 15% to about 70%, from about 20% to about 70%, from about 25% to about 70%, from about 30% to about 70%, from about 35% to about 70%, from about 40% to about 70%, from about 5% to about 65%, from about 10% to about 65%, from about 15% to about 65%, from about 20% to about 65%, from about 25% to about 65%, from about 30% to about 65%, from about 35% to about 65%, from about 40% to about 65%, from about 5% to about 60%, from about 10% to about 60%, from about 15% to about 60%, from about 20% to about 60%, from about 25% to about 60%, from about 30% to about 60%, from about 35% to about 60%, from about 40% to about 60%, or about 50%, the remainder comprising the corresponding non-human donor residue at the designated position.

In certain embodiments, it may be preferable to reduce the content of certain amino acids that impart chemical instability or heterogeneity problems, such as methionine, aspartic acid, tryptophan, asparagine, cysteine, tryptophan. Often, these residues are involved in post-transcriptional modifications, such as glycosylation, methylation, acetylation, oxidation, acid hydrolysis and deamination. Certain types of post-transcriptional modifications may be undesirable.

For example, as shown in FIG. 1, the human residue at position 53 of CDR-L2 is S, and the rat residue is N. If desired, the percentage of library clones incorporating N may be reduced to significantly below 50% to minimize the risk of generating daughter clones with deamidation or glycosylation motifs. For example, synthesis may be carried out such that only about 1-2% of the clones have N, and 98-99% of the clones have S. Other circumstances where one may not wish to achieve a 50:50 distribution of human: non-human amino acids at given positions could be to avoid the generation of structural motifs that affect protein drug development such as surface charge patches, and/or hydrophobicity patches.

For CDR-H3, each position can be any one of the 20 natural amino acid residues. In certain embodiments, it may be desirable that for each position, each of the 20 natural amino acid residues are substantially equally represented in the library (i.e., about 5% the library clones incorporate one particular amino acid). Again, because synthesis biases, substantially equal distribution of the 20 residues may not be achieve, and in many cases, is not necessary. Accordingly, in certain embodiments, for each position within CDR-H3, each of the 20 amino acid residues is represented by at least about 0.1% (e.g., at least about 0.1%, at least about 0.2%, at least about 0.5%, at least about 0.8%, at least about 1%, at least about 1.5%, at least about 2%, at least about 2.5%, at least about 3%, at least about 3.5%, at least about 4%, or at least about 4.5%) of the polypeptides in the library. In certain embodiments, for each position within CDR-H3, each of the 20 amino acid residues is represented by from about 0.1% to about 20% (e.g., from about 0.1% to about 20%, from about 0.1% to about 15%, from about 0.1% to about 10%, from about 0.2% to about 20%, from about 0.2% to about 15%, from about 0.2% to about 10%, from about 0.5% to about 20%, from about 0.5% to about 15%, from about 0.5% to about 10%, from about 0.8% to about 20%, from about 0.8% to about 15%, from about 0.8% to about 10%, from about 1% to about 20%, from about 1% to about 15%, from about 1% to about 10%, from about 2% to about 20%, from about 2% to about 15%, from about 2% to about 10%, from about 3% to about 20%, from about 3% to about 15%, from about 3% to about 10%, from about 4% to about 20%, from about 4% to about 15%, from about 4% to about 10%, from about 0.1% to about 9%, from about 0.2% to about 9%, from about 0.5% to about 9%, from about 0.8% to about 9%, from about 1% to about 9%, from about 2% to about 9%, from about 3% to about 9%, from about 4% to about 9%, from about 0.1% to about 8%, from about 0.2% to about 8%, from about 0.5% to about 8%, from about 0.8% to about 8%,from about 1% to about 8%, from about 2% to about 8%, from about 3% to about 8%, from about 4% to about 8%, from about 0.1% to about 7%, from about 0.2% to about 7%, from about 0.5% to about 7%, from about 0.8% to about 7%, from about 1% to about 7%, from about 2% to about 7%, from about 3% to about 7%, from about 4% to about 7%, from about 0.1% to about 6%, from about 0.2% to about 6%, from about 0.5% to about 6%, from about 0.8% to about 6%, from about 0.1% to about 6%, from about 0.2% to about 6%, from about 0.5% to about 6%, from about 0.8% to about 6%, from about 1% to about 6%, from about 2% to about 6%, from about 3% to about 6%, or from about 4% to about 6%) of the polypeptides in the library.

In certain embodiments, it may be preferable to reduce the content of certain amino acids in CDR-H3 that impart chemical instability or heterogeneity problems such as methionine, aspartic acid, tryptophan, asparagine, cysteine, tryptophan, as described above.

Often it is not necessary for the library to incorporate all 20 natural amino acids at each position within CDR-H3. Since conservative substitutions are generally well tolerated, certain residues may be omitted from the library. For example, since Gin is a conservative substitution of Asn, the library can omit Asn in CDR-H3, and use Gin instead. Sometimes it may be desirable to increase the percentage of Gin if Asn is replaced with Gin in CDR-H3. Other conservative substitutions can be similarly used to omit certain residues.

TABLE 12 Conservative Conservative Residue substitution Residue substitution Ala Ser Leu Ile, Val Arg Lys Lys Arg, Gln Asn Gln; His Met Leu, Ile Asp Glu Phe Met, Leu, Tyr Cys Ser Ser Thr; Gly Gln Asn Thr Ser, Val Glu Asp Trp Tyr Gly Pro Tyr Trp, Phe His Asn, Gln Val Ile, Leu Ile Leu, Val Pro —

Methods of incorporating both human and non-human residues (CDR-L1, CDR-L2, CDR-L3, CDR-H1, and CDR-H3) and 20 natural amino acid residues (CDR-H3) into a combinatorial library are generally known, for example, by amplifying VH sequence by PCR, and/or performing random mutagenesis in CDR3.

The libraries disclosed herein can be used to screen for “ultra” humanized antibodies, in particular antibodies where human germline residues are incorporated into non-human donor CDRs. Accordingly, also provided herein is humanized antibody or antigen-binding fragment thereof that binds to a target antigen, wherein human germline residues are incorporated into CDRs.

In certain embodiments, the human germline VL framework is the framework of DPK9 (IMGT name: IGKV1-39), and for each position within CDR-L1, CDR-L2, and CDR-L3, the residue is either the respective human residue shown below, or its corresponding residue from the non-human donor antibody:

TABLE 13 SEQ ID NO. Light Chain 410 CDR-L1 RASQSISSYLN 411 CDR-L2 AASSLQS 412 CDR-L3 QQSYSTP

In certain embodiments, the human germline VL framework is the framework of DPK12 (IMGT name: IGKV2D-29), and for each position within CDR-L1, CDR-L2, and CDR-L3, the residue is either the respective human residue shown below, or its corresponding residue from the non-human donor antibody:

TABLE 14 SEQ ID NO. Light Chain 413 CDR-L1 KSSQSLLHSDGKTYLY 414 CDR-L2 EVSNRFS 415 CDR-L3 MQSIQLP

In certain embodiments, the human germline VL framework is the framework of DPK18 (IMGT name: IGKV2-30), and for each position within CDR-L1, CDR-L2, and CDR-L3, the residue is either the respective human residue shown below, or its corresponding residue from the non-human donor antibody:

TABLE 15 SEQ ID NO. Light Chain 416 CDR-L1 RSSQSLVYSDGNTYLN 417 CDR-L2 KVSNRDS 418 CDR-L3 MQGTHWP

In certain embodiments, the human germline VL framework is the framework of DPK24 (IMGT name: IGKV4-1), and for each position within CDR-L1, CDR-L2, and CDR-L3, the residue is either the respective human residue shown below, or its corresponding residue from the non-human donor antibody:

TABLE 16 SEQ ID NO. Light Chain 419 CDR-L1 KSSQSVLYSSNNKNYLA 420 CDR-L2 WASTRES 421 CDR-L3 QQYYSTP

In certain embodiments, the human germline VL framework is the framework of HK102_V1 (IMGT name: IGKV1-5), and for each position within CDR-L1, CDR-L2, and CDR-L3, the residue is either the respective human residue shown below, or its corresponding residue from the non-human donor antibody:

TABLE 17 SEQ ID NO. Light Chain 422 CDR-L1 RASQSISSWLA 423 CDR-L2 DASSLES 424 CDR-L3 QQYNSYS

In certain embodiments, the human germline VL framework is the framework of DPK1 (IMGT name: IGKV1-33), and for each position within CDR-L1, CDR-L2, and CDR-L3, the residue is either the respective human residue shown below, or its corresponding residue from the non-human donor antibody:

TABLE 18 SEQ ID NO. Light Chain 425 CDR-L1 QASQDISNYLN 426 CDR-L2 DASNLET 427 CDR-L3 QQYDNLP

In certain embodiments, the human germline VL framework is the framework of DPK8 (IMGT name: IGKV1-9), and for each position within CDR-L1, CDR-L2, and CDR-L3, the residue is either the respective human residue shown below, or its corresponding residue from the non-human donor antibody:

TABLE 19 SEQ ID NO. Light Chain 428 CDR-L1 RASQGISSYLA 429 CDR-L2 AASTLQS 430 CDR-L3 QQLNSYP

In certain embodiments, the human germline VL framework is the framework of DPK21 (IMGT name: IGKV3-15), and for each position within CDR-L1, CDR-L2, and CDR-L3, the residue is either the respective human residue shown below, or its corresponding residue from the non-human donor antibody:

TABLE 20 SEQ ID NO. Light Chain 431 CDR-L1 RASQSVSSNLA 432 CDR-L2 GASTRAT 433 CDR-L3 QQYNNWP

In certain embodiments, the human germline VL framework is the framework of Vg_38K (IMGT name: IGKV3-11), and for each position within CDR-L1, CDR-L2, and CDR-L3, the residue is either the respective human residue shown below, or its corresponding residue from the non-human donor antibody:

TABLE 21 SEQ ID NO. Light Chain 434 CDR-L1 RASQSVSSYLA 435 CDR-L2 DASNRAT 436 CDR-L3 QQRSNWP

In certain embodiments, the human germline VL framework is the framework of DPK22 (IMGT name: IGKV3-20), and for each position within CDR-L1, CDR-L2, and CDR-L3, the residue is either the respective human residue shown below, or its corresponding residue from the non-human donor antibody:

TABLE 22 SEQ ID NO. Light Chain 437 CDR-L1 RASQSVSSSYLA 438 CDR-L2 GASSRAT 439 CDR-L3 QQYGSSP

In certain embodiments, the human germline VL framework is the framework of DPK15 (IMGT name: IGKV2-28), and for each position within CDR-L1, CDR-L2, and CDR-L3, the residue is either the respective human residue shown below, or its corresponding residue from the non-human donor antibody:

TABLE 23 SEQ ID NO. Light Chain 440 CDR-L1 RSSQSLLHSNGYNYLD 441 CDR-L2 LGSNRAS 442 CDR-L3 MQALQTP

In certain embodiments, the human germline VL framework is the framework of DPL16 (IMGT name: IGLV3-19), and for each position within CDR-L1, CDR-L2, and CDR-L3, the residue is either the respective human residue shown below, or its corresponding residue from the non-human donor antibody:

TABLE 24 SEQ ID NO. Light Chain 443 CDR-L1 QGDSLRSYYAS 444 CDR-L2 GKNNRPS 445 CDR-L3 NSRDSSGNH

In certain embodiments, the human germline VL framework is the framework of DPL8 (IMGT name: IGLV1-40), and for each position within CDR-L1, CDR-L2, and CDR-L3, the residue is either the respective human residue shown below, or its corresponding residue from the non-human donor antibody:

TABLE 25 SEQ ID NO. Light Chain 446 CDR-L1 TGSSSNIGAGYDVH 447 CDR-L2 GNSNRPS 448 CDR-L3 QSYDSSLSG

In certain embodiments, the human germline VL framework is the framework of V1-22 (IMGT name: IGLV6-57), and for each position within CDR-L1, CDR-L2, and CDR-L3, the residue is either the respective human residue shown below, or its corresponding residue from the non-human donor antibody:

TABLE 26 SEQ ID NO. Light Chain 449 CDR-L1 TRSSGSIASNYVQ 450 CDR-L2 EDNQRPS 451 CDR-L3 QSYDSSN

In certain embodiment, the human germline VL framework is the framework of human Vλ consensus sequence, and for each position within CDR-L1, CDR-L2, and CDR-L3, the residue is either the respective human residue shown below, or its corresponding residue from the non-human donor antibody. Alternative sequences are provided for the consensus sequence with and without gaps. At positions where there is no consensus, residues in ( ) are those that are tied for the most frequent residues.

TABLE 27 SEQ ID NO. Light Chain 452 CDR-L1 TGSSSGGSYYVS or 453 TGSSSDVGGSYYVS 454 CDR-L2 ENDSNRPS or 455 EDSNR(S/D)K(Q/G)QKPS 456 CDR-L3 QSWDSSA(N/T) or 457 QSWDSSA(N/T)F(F/V)(G/V)

In certain embodiment, the human germline VL framework is the framework of human Vλ1 consensus sequence, and for each position within CDR-L1, CDR-L2, and CDR-L3, the residue is either the respective human residue shown below, or its corresponding residue from the non-human donor antibody. Alternative sequences are provided for the consensus sequence with and without gaps. At positions where there is no consensus, residues in ( ) are those that are tied for the most frequent residues.

TABLE 28 SEQ ID NO. Light Chain 458 CDR-L1 SGSSSNIGNN(A/Y)V(N/H/S) or 459 SGSSSNIIGNN(A/Y)V(N/H/S) 460 CDR-L2 GNN(K/N/Q)RPS 461 CDR-L3 AAWDDSL(N/S)G

In certain embodiment, the human germline VL framework is the framework of human Vλ3 consensus sequence, and for each position within CDR-L1, CDR-L2, and CDR-L3, the residue is either the respective human residue shown below, or its corresponding residue from the non-human donor antibody. Alternative sequences are provided for the consensus sequence with and without gaps. At positions where there is no consensus, residues in ( ) are those that are tied for the most frequent residues.

TABLE 29 SEQ ID NO. Light Chain 462 CDR-L1 CSGD(A/V)LG(K/S)KYAH 463 CDR-L2 KDSERPS 464 CDR-L3 QSWDSSG(N/D/T/A) or 465 QSWDSSG(N/D/T/A)H

In certain embodiment, the human germline VL framework is the framework of human VK consensus sequence, and for each position within CDR-L1, CDR-L2, and CDR-L3, the residue is either the respective human residue shown below, or its corresponding residue from the non-human donor antibody. Alternative sequences are provided for the consensus sequence with and without gaps.

TABLE 30 SEQ ID NO. Light Chain 466 CDR-L1 RASQSLLHSDGISSYLA or 467 RASQGISSYLA 468 CDR-L2 AASSRAS 469 CDR-L3 QQYNSYP

In certain embodiment, the human germline VL framework is the framework of human VK1 consensus sequence, and for each position within CDR-L1, CDR-L2, and CDR-L3, the residue is either the respective human residue shown below, or its corresponding residue from the non-human donor antibody. At positions where there is no consensus, residues in ( ) are those that are tied for the most frequent residues.

TABLE 31 SEQ ID NO. Light Chain 470 CDR-L1 RASQGIS(N/S)YLA 471 CDR-L2 AASSLQS 472 CDR-L3 QQYNSYP

In certain embodiment, the human germline VL framework is the framework of human VK2 consensus sequence, and for each position within CDR-L1, CDR-L2, and CDR-L3, the residue is either the respective human residue shown below, or its corresponding residue from the non-human donor antibody. Alternative sequences are provided for the consensus sequence with and without gaps. At positions where there is no consensus, residues in ( ) are those that are tied for the most frequent residues.

TABLE 32 SEQ ID NO. Light Chain 473 CDR-L1 RSSQSLLHSDGNTYLD or 474 RSSQSLLHSDDGNTYLD 475 CDR-L2 (K/T)(V/I)SNR(A/F)S 476 CDR-L3 MQATQFP

In certain embodiment, the human germline VL framework is the framework of human VK3 consensus sequence, and for each position within CDR-L1, CDR-L2, and CDR-L3, the residue is either the respective human residue shown below, or its corresponding residue from the non-human donor antibody. At positions where there is no consensus, residues in ( ) are those that are tied for the most frequent residues.

TABLE 33 SEQ ID NO. Light Chain 477 CDR-L1 RASQS(S/V)(S/V)SSYLA 478 CDR-L2 GASTRAT 479 CDR-L3 QQY(S/N/G/H)NWP

In certain embodiments, the human germline VH framework is the framework of DP54 or IGHV3-7, and for each position within CDR-H1, and CDR-H2, the residue is either the respective human residue shown below, or its corresponding residue from the non-human donor antibody:

TABLE 34 SEQ ID NO. Heavy Chain 480 CDR-H1 GFTFSSYWMS 481 CDR-H2 ANIKQDGSEKYYVDSVKG

In certain embodiments, the human germline VH framework is the framework of DP47 or IGHV3-23 and for each position within CDR-H1, and CDR-H2, the residue is either the respective human residue shown below, or its corresponding residue from the non-human donor antibody:

TABLE 35 SEQ ID NO. Heavy Chain 482 CDR-H1 GFTFSSYAMS 483 CDR-H2 AISGSGGSTYYADSVKG

In certain embodiments, the human germline VH framework is the framework of DP71 or IGHV4-59 and for each position within CDR-H1, and CDR-H2, the residue is either the respective human residue shown below, or its corresponding residue from the non-human donor antibody:

TABLE 36 SEQ ID NO. Heavy Chain 484 CDR-H1 GGSISSYYWS 485 CDR-H2 GYIYYSGSTNYNPSLKS

In certain embodiments, the human germline VH framework is the framework of DP75 or IGHV1-2_02 and for each position within CDR-H1, and CDR-H2, the residue is either the respective human residue shown below, or its corresponding residue from the non-human donor antibody:

TABLE 37 SEQ ID NO. Heavy Chain 486 CDR-H1 GYTFTGYYMH 487 CDR-H2 GWINPNSGGTNYAQKFQG

In certain embodiments, the human germline VH framework is the framework of DP10 or IGHV1-69 and for each position within CDR-H1, and CDR-H2, the residue is either the respective human residue shown below, or its corresponding residue from the non-human donor antibody:

TABLE 38 SEQ ID NO. Heavy Chain 488 CDR-H1 GGTFSSYAIS 489 CDR-H2 GGIIPIFGTANYAQKFQG

In certain embodiments, the human germline VH framework is the framework of DP7 or IGHV1-46, and for each position within CDR-H1, and CDR-H2, the residue is either the respective human residue shown below, or its corresponding residue from the non-human donor antibody:

TABLE 39 SEQ ID NO. Heavy Chain 490 CDR-H1 GYTGTSYYMH 491 CDR-H2 GIINPSGGSTSYAQKFQG

In certain embodiments, the human germline VH framework is the framework of DP49 or IGHV3-30, and for each position within CDR-H1, and CDR-H2, the residue is either the respective human residue shown below, or its corresponding residue from the non-human donor antibody:

TABLE 40 SEQ ID NO. Heavy Chain 492 CDR-H1 GFTFSSYGMH 493 CDR-H2 AVISYDGSNKYYADSVKG

In certain embodiments, the human germline VH framework is the framework of DP51 or IGHV3-48, and for each position within CDR-H1, and CDR-H2, the residue is either the respective human residue shown below, or its corresponding residue from the non-human donor antibody:

TABLE 41 SEQ ID NO. Heavy Chain 494 CDR-H1 GFTFSSYSMN 495 CDR-H2 SYISSSSSTIYYADSVKG

In certain embodiments, the human germline VH framework is the framework of DP38 or IGHV3-15, and for each position within CDR-H1, and CDR-H2, the residue is either the respective human residue shown below, or its corresponding residue from the non-human donor antibody:

TABLE 42 SEQ ID NO. Heavy Chain 496 CDR-H1 GFTFSNAWMS 497 CDR-H2 GRIKSKTDGGTTDYAAPVKG

In certain embodiments, the human germline VH framework is the framework of DP79 or IGHV4-39, and for each position within CDR-H1, and CDR-H2, the residue is either the respective human residue shown below, or its corresponding residue from the non-human donor antibody:

TABLE 43 SEQ ID NO. Heavy Chain 498 CDR-H1 GGSISSSSYYWG 499 CDR-H2 GSIYYSGSTYYNPSLKS

In certain embodiments, the human germline VH framework is the framework of DP78 or IGHV4-30-4, and for each position within CDR-H1, and CDR-H2, the residue is either the respective human residue shown below, or its corresponding residue from the non-human donor antibody:

TABLE 44 SEQ ID NO. Heavy Chain 500 CDR-H1 GGSISSGDYYWS 501 CDR-H2 GYIYYSGSTYYNPSLKS

In certain embodiments, the human germline VH framework is the framework of DP73 or IGHV5-51, and for each position within CDR-H1, and CDR-H2, the residue is either the respective human residue shown below, or its corresponding residue from the non-human donor antibody:

TABLE 45 SEQ ID NO. Heavy Chain 502 CDR-H1 GYSFTSYWIG 503 CDR-H2 GIIYPGDSDTRYSPSFQG

In certain embodiments, the human germline VH framework is the framework of human VH germline consensus sequence and for each position within CDR-H1, and CDR-H2, the residue is either the respective human residue shown below, or its corresponding residue from the non-human donor antibody. Alternative sequences are provided for the consensus sequence with and without gaps. At positions where there is no consensus, residues in ( ) are those that are tied for the most frequent residues.

TABLE 46 SEQ ID NO. Heavy Chain 504 CDR-H1 GFTFSSYAM(H/S) or 505 GFTFSSYAM(H/S)WS 506 CDR-H2 GWISPNGGSTYYADSVKG or 507 GWISPKANGGSTYYADSVKG

In certain embodiments, the human germline VH framework is the framework of human VH3 germline consensus sequence, and for each position within CDR-H1, and CDR-H2, the residue is either the respective human residue shown below, or its corresponding residue from the non-human donor antibody. Alternative sequences are provided for the consensus sequence with and without gaps. At positions where there is no consensus, residues in ( ) are those that are tied for the most frequent residues.

TABLE 47 SEQ ID NO. Heavy Chain 508 CDR-H1 GFTFSSYAMS 509 CDR-H2 SVISSDG(G/S)STYYADSVKG or 510 SVISSKADG(G/S)STYYADSVKG

In certain embodiments, the human germline VH framework is the framework of human VH5 germline consensus sequence, and for each position within CDR-H1, and CDR-H2, the residue is either the respective human residue shown below, or its corresponding residue from the non-human donor antibody. At positions where there is no consensus, residues in ( ) are those that are tied for the most frequent residues.

TABLE 48 SEQ ID NO. Heavy Chain 511 CDR-H1 GYSFTSYWI(S/G/H) 512 CDR-H2 G(R/I/S)IYPGDSDTRYSPSFQG

In certain embodiments, the human germline VH framework is the framework of human VH1 germline consensus sequence, and for each position within CDR-H1, and CDR-H2, the residue is either the respective human residue shown below, or its corresponding residue from the non-human donor antibody. At positions where there is no consensus, residues in ( ) are those that are tied for the most.

TABLE 49 SEQ ID NO. Heavy Chain 513 CDR-H1 GYTFTSY(A/Y)(I/M)H 514 CDR-H2 GWINP(G/Y)NGNTNYAQKFQ

In certain embodiments, the human germline VH framework is the framework of human VH4 germline consensus sequence, and for each position within CDR-H1, and CDR-H2, the residue is either the respective human residue shown below, or its corresponding residue from the non-human donor antibody. At positions where there is no consensus, residues in ( ) are those that are tied for the most frequent residues.

TABLE 50 SEQ ID NO. Heavy Chain 515 CDR-H1 GGSISSG(N/Y)YYWS 516 CDR-H2 GYIYYSGSTYYNPSLKS

For example, if the framework sequence of human germline DPK9 is used as an acceptor for humanization, and the non-human donor CDR-L1 sequence is RASQDVGIYVN (SEQ ID NO: 2), then the CDR-L1 of the resulting humanized antibody or antigen-binding fragment should be: RASQ(S/D)(IN)(S/G)(S/I)Y(L/V)N(SEQ ID NO:518). If the framework sequence of human germline DPL16 is used as an acceptor for humanization, and the non-human donor CDR-L1 sequence is RASQDVGIYVN (SEQ ID NO: 2), then the CDR-L1 of the resulting humanized antibody or antigen-binding fragment should be: (Q/R)(G/A)(D/S)(S/Q)(L/D)(RN)(S/G)(Y/I)Y(AN)(S/N) (SEQ ID NO:518). Under this design rationale, once a specific human germline sequence is selected as an acceptor, then five of the six CDR can be readily designed, as each individual position generally only has two choices—the germline residue from the same human germline, or the corresponding donor residue.

As shown in the Examples, certain positions in CDRs prefer non-human donor residues, whereas certain positions in CDRs tolerate human germline residues well. Positions that generally tolerate human germline residues well are candidates for CDR humanization. For example, as shown in FIG. 10, the n-terminal 4 residues of the VK CDR1, and last 6 residues of the VH CDR2 showed low retention rate of non-human donor residues. This indicates that these residues are candidates for CDR humanization.

Accordingly, provided herein are humanized antibodies or antigen-binding fragment thereof (such as an antibody variable domain), and libraries comprising such antibodies or antigen-binding fragment thereof (such as an antibody variable domain), wherein one or more of the n-terminal 4 residues of CDR-L1 (residues 24, 25, 26, and 27 respectively, based on Kabat numbering) comprise the corresponding human germline residues. In certain embodiments, the light chain framework sequence is from a human VK germline.

Also provided herein are humanized antibodies or antigen-binding fragment thereof (such as an antibody variable domain), and libraries comprising such antibodies or antigen-binding fragment thereof (such as an antibody variable domain), wherein one or more of the last 6 residues of CDR-H2 (residues 60, 61, 62, 63, 64, 65 respectively, based on Kabat numbering) comprise the corresponding human germline residues. In certain embodiments, the heavy chain framework sequence is from a human VH3 germline, VH1 germline, VH5 germline, or VH4 germline.

D. Antibody Display

The antibody libraries described herein are generally screened to identify specific clones that show desired antigen-binding affinities, or other properties (e.g., potency). For screening, a variety of techniques may be used to display these antibody variable domains.

Commonly used display libraries include, e.g., phage display, yeast display, mammalian cell surface display, bacterial display, viral display, mRNA display, ribosome display or DNA display library.

One exemplary display library is a phage display library. Phage display is a technique by which variant polypeptides are displayed as fusion proteins to a coat protein on the surface of phage, e.g., filamentous phage, particles. One advantage of phage display library is that large libraries of randomized protein variants can be rapidly and efficiently sorted for those sequences that bind to a target molecule with high affinity. Polyvalent phage display methods have been used for displaying small random peptides and small proteins through fusions to either gene III or gene VIII of filamentous phage. Wells and Lowman, Curr Opin Struct Biol, 3:355-362 (1992). In monovalent phage display, a protein or peptide library is fused to a gene III or a portion thereof, and expressed at low levels in the presence of wild type gene III protein so that phage particles display one copy or none of the fusion proteins. Avidity effects are reduced relative to polyvalent phage so that sorting is on the basis of intrinsic ligand affinity, and phagemid vectors are used, which simplify DNA manipulations. Lowman and Wells, Methods: A companion to Methods in Enzymology, 3:205-0216 (1991).

A phagemid is a plasmid vector having a bacterial origin of replication, e.g., ColE1, and a copy of an intergenic region of a bacteriophage. The phagemid may be used on any known bacteriophage, including filamentous bacteriophage and lambdoid bacteriophage. The plasmid will also generally contain a selectable marker for antibiotic resistance. Segments of DNA cloned into these vectors can be propagated as plasmids. When cells harboring these vectors are provided with all genes necessary for the production of phage particles, the mode of replication of the plasmid changes to rolling circle replication to generate copies of one strand of the plasmid DNA and package phage particles. The phagemid may form infectious or non-infectious phage particles. Phagemids may contain a phage coat protein gene or fragment thereof linked to a heterologous polypeptide gene as a gene fusion such that the heterologous polypeptide is displayed on the surface of the phage particle.

A phage vector is a double stranded replicative form of a bacteriophage containing a heterologous gene and capable of replication. The phage vector has a phage origin of replication allowing phage replication and phage particle formation. The phage is preferably a filamentous bacteriophage, such as an M13, f1, fd, Pf3 phage or a derivative thereof, or a lambdoid phage, such as lambda, phage 21, phi80, phi81, 82, 424, 434, or a derivative thereof.

A phage vector may also encode a tag, for example, a polyhistidine tag, to facilitate the detection or identification of antibody variable domains that bind to a specific antigen.

4. Screening and Selection of Antibodies

The displayed antibody variable domains can then be screened for, e.g., the ability to bind the target antigen. For example, the target antigen can be attached with a detectable moiety, such as biotin. Polypeptides that bind to the target antigen can be separated from unbound ones by a molecule that binds to the detectable moiety, such as streptavidin-coated beads where biotin is the detectable moiety. Affinity of binders (polypeptide that binds to target) can be determined based on concentration of the target molecule used, using formulas and based on criteria known in the art.

The target antigen may also be attached to a suitable matrix such as agarose beads, acrylamide beads, glass beads, cellulose, various acrylic copolymers, hydroxyalkyl methacrylate gels, polyacrylic and polymethacrylic copolymers, nylon, neutral and ionic carriers, and the like. After attachment of the target antigen to the matrix, the immobilized target is contacted with the antibody library. Polypeptides bound to the immobilized antigen can then be separated from those that do not bind to the target by washing.

The binders can be isolated and then re-amplified or expressed in a host cell, and subjected to additional rounds of selection for binding of target molecules. Any number of rounds of selection or sorting can be utilized.

In certain embodiments, the library is screened to select a polypeptide that binds to the target antigen, with an affinity (Kd) value of no more than about 1×10⁻³ M, such as no more than about 1×10⁻³ M, no more than about 9×10⁻⁴ M, no more than about 8×10⁻⁴ M, no more than about 7×10⁻⁴ M, no more than about 6×10⁻⁴ M, no more than about 5×10⁻⁴M, no more than about 4×10⁻⁴ M, no more than about 3×10⁻⁴ M, no more than about 2×10⁻⁴ M, no more than about 1×10⁻⁴ M, no more than about 9×10⁻⁵ M, no more than about 8×10⁻⁵ M, no more than about 7×10⁻⁵ M, no more than about 6×10⁻⁵ M, no more than about 5×10⁻⁵ M, no more than about 4×10⁻⁵ M, no more than about 3×10⁻⁵ M, no more than about 2×10⁻⁵ M, no more than about 1×10⁻⁵ M, no more than about 9×10⁻⁶ M, no more than about 8×10⁻⁶ M, no more than about 7×10⁻⁶ M, no more than about 6×10⁻⁶ M, no more than about 5×10⁻⁶ M, no more than about 4×10⁻⁶ M, no more than about 3×10⁻⁶ M, no more than about 2×10⁻⁶ M, no more than about 1×10⁻⁶ M, no more than about 9×10⁻⁷ M, no more than about 8×10⁻⁷ M, no more than about 7×10⁻⁷ M, no more than about 6×10⁻⁷ M, no more than about 5×10⁻⁷ M, no more than about 4×10⁻⁷ M, no more than about 3×10⁻⁷ M, no more than about 2×10⁻⁷ M, no more than about 1×10⁻⁷ M, no more than about 9×10⁻⁸ M, no more than about 8×10⁻⁸ M, no more than about 7×10⁻⁸M, no more than about 6×10⁻⁸ M, no more than about 5×10⁻⁸ M, no more than about 4×10⁻⁸ M, no more than about 3×10⁻⁸ M, no more than about 2×10⁻⁸ M, no more than about 1×10⁻⁸ M, no more than about 9×10⁻⁹ M, no more than about 8×10⁻⁹ M, no more than about 7×10⁻⁹ M, no more than about 6×10⁻⁹ M, no more than about 5×10⁻⁹ M, no more than about 4×10⁻⁹ M, no more than about 3×10⁻⁹ M, no more than about 2×10⁻⁹ M, no more than about 1×10⁻⁹ M, from about 1×10⁻³ M to about 1×10⁻¹³ M, 1×10⁻⁴ M to about 1×10⁻¹³ M, 1×10⁻⁵M to about 1×10⁻¹³ M, from about 1×10⁻⁶ M to about 1×10⁻¹³M, from about 1×10⁻⁷ M to about 1×10⁻¹³ M, from about 1×10⁻⁸ M to about 1×10⁻¹³ M, from about 1×10⁻⁹ M to about 1×10⁻¹³ M, 1×10⁻³ M to about 1×10⁻¹² M, 1×10⁻⁴ M to about 1×10⁻¹² M, from about 1×10⁻⁵ M to about 1×10⁻¹² M, from about 1×10⁻⁶ M to about 1×10⁻¹² M, from about 1×10⁻⁷ M to about 1×10⁻¹² M, from about 1×10⁻⁸ M to about 1×10⁻¹² M, from about 1×10⁻⁹ M to about 1×10⁻¹² M, 1×10⁻³ M to about 1×10¹¹ M, 1×10⁻⁴M to about 1×10¹¹ M, from about 1×10⁻⁵ M to about 1×10¹¹ M, from about 1×10⁻⁶ M to about 1×10⁻¹¹ M, from about 1×10⁻⁷ M to about 1×10⁻¹¹ M, from about 1×10⁻⁸ M to about 1×10¹¹ M, from about 1×10⁻⁹ M to about 1×10⁻¹¹ M, 1×10⁻³ M to about 1×10⁻¹⁰ M, 1×10⁻⁴M to about 1×10⁻¹⁰ M, from about 1×10⁻⁵ M to about 1×10⁻¹⁰ M, from about 1×10⁻⁶ M to about 1×10⁻¹⁰ M, from about 1×10⁻⁷ M to about 1×10⁻¹⁰ M, from about 1×10⁻⁸M to about 1×10¹⁰ M, or from about 1×10⁻⁹M to about 1×10¹⁰ M.

In certain embodiments, a polypeptide that binds to the target antigen with a binding affinity (Kd) value that is equal or less than the binding affinity (Kd) value of the original non-human donor antibody.

Although in general, Kd at nanomolar range is desired, in certain embodiments, low affinity antibodies may be preferred, for example, for targeting highly expressed receptors in compartments and avoiding off-target binding. Further, some therapeutic applications may benefit from an antibody with lower binding affinity to facilitate antibody recycling.

In certain embodiments, the selected antibody variable domains may also be further screened by other biological activity assays, e.g., in order to evaluate its potency, pharmacological activity, and potential efficacy as a therapeutic agent. Such assays are known in the art and depend on the target antigen and intended use for the antibody. Examples include e.g., tumor cell growth inhibition assays; antibody-dependent cellular cytotoxicity (ADCC) and complement-mediated cytotoxicity (CDC) assays; agonistic activity or antagonist activity assays.

Once a desired clone is selected, the sequence of the antibody variable domain, and nucleic acid encoding such antibody variable domain, can be determined using standard sequencing techniques. Nucleic acid sequence encoding a desired antibody variable domain may be inserted into other vectors (such as cloning and expression vectors) for recombinant production and characterization.

Suitable cloning and expression vectors can include a variety of components, such as promoter, enhancer, and other transcriptional regulatory sequences. The vector may also be constructed to allow for movement of antibody variable domain between different vectors.

Selected antibody (or antigen-binding fragment thereof) may be made recombinantly produced using a suitable host cell. Nucleic acid encoding the antibody or antigen-binding fragment thereof can be cloned into an expression vector, which can then be into a host cell, such as E. coli cell, a yeast cell, an insect cell, a simian COS cell, a Chinese hamster ovary (CHO) cell, or a myeloma cell that do not otherwise produce immunoglobulin protein, to obtain the synthesis of monoclonal antibodies in the recombinant host cells.

Antibody fragments can be produced by proteolytic or other degradation of the antibodies, by recombinant methods, or by chemical synthesis. Polypeptides of the antibodies, especially shorter polypeptides up to about 50 amino acids, are conveniently made by chemical synthesis. Methods of chemical synthesis are known in the art and are commercially available.

The selected antibody or antigen-binding fragment thereof may be affinity-matured. For example, affinity matured antibodies can be produced by procedures known in the art (Marks et al., 1992, Bio/Technology, 10:779-783; Barbas et al., 1994, Proc Nat. Acad. Sci, USA 91:3809-3813; Schier et al., 1995, Gene, 169:147-155; Yelton et al., 1995, J. Immunol., 155:1994-2004; Jackson et al., 1995, J. Immunol., 154(7):3310-9; Hawkins et al., 1992, J. Mol. Biol., 226:889-896; and WO2004/058184).

5. Formulations and Uses

Antibodies or antigen-binding fragments identified from the library described herein can be formulated as pharmaceutical formulations. The pharmaceutical formulation may further comprise pharmaceutically acceptable carriers, excipients, or stabilizers (Remington: The Science and practice of Pharmacy 20th Ed., 2000, Lippincott Williams and Wilkins, Ed. K. E. Hoover), in the form of lyophilized formulations or aqueous solutions. Acceptable carriers, excipients, or stabilizers are nontoxic to recipients at the dosages and concentrations, and may comprise buffers such as phosphate, citrate, and other organic acids; antioxidants including ascorbic acid and methionine; preservatives (such as octadecyldimethylbenzyl ammonium chloride; hexamethonium chloride; benzalkonium chloride, benzethonium chloride; phenol, butyl or benzyl alcohol; alkyl parabens such as methyl or propyl paraben; catechol; resorcinol; cyclohexanol; 3-pentanol; and m-cresol); low molecular weight (less than about 10 residues) polypeptides; proteins, such as serum albumin, gelatin, or immunoglobulins; hydrophilic polymers such as polyvinylpyrrolidone; amino acids such as glycine, glutamine, asparagine, histidine, arginine, or lysine; monosaccharides, disaccharides, and other carbohydrates including glucose, mannose, or dextrans; chelating agents such as EDTA; sugars such as sucrose, mannitol, trehalose or sorbitol; salt-forming counter-ions such as sodium; metal complexes (e.g. Zn-protein complexes); and/or non-ionic surfactants such as TWEEN™, PLURONICS™ or polyethylene glycol (PEG). Pharmaceutically acceptable excipients are further described herein.

The antibodies or antigen-binding fragments identified from the library described herein can be used for therapeutic, diagnostic, or non-therapeutic purposes. For example, the antibody or antigen-binding fragment thereof may be used as an affinity purification agents (e.g., for in vitro purification), as a diagnostic agent (e.g., for detecting expression of an antigen of interest in specific cells, tissues, or serum)

For therapeutic applications, antibodies or antigen-binding fragments identified from the library described herein can be administered to a mammal, especially a human by conventional techniques, such as intravenously (as a bolus or by continuous infusion over a period of time), intramuscularly, intraperitoneally, intra-cerebrospinally, subcutaneously, intra-articularly, intrasynovially, intrathecally, orally, topically, or by inhalation. The antibodies or antigen-binding fragments also are suitably administered by intra-tumoral, peri-tumoral, intra-lesional, or peri-lesional routes. The antibodies or antigen-binding fragments can be used in prophylactic treatment or therapeutic treatment.

EXAMPLES

The invention is further described in detail by reference to the following experimental examples. These examples are provided for purposes of illustration only, and are not intended to be limiting unless otherwise specified. Thus, the invention should in no way be construed as being limited to the following examples, but rather, should be construed to encompass any and all variations which become evident as a result of the teaching provided herein.

Current evidence suggests that the main risk factors for antibody immunogenicity in man are human t-cell epitope content and, to a lesser extent, t-cell independent b-cell responses. B-cell epitopes are challenging to predict and b-cell-only responses to biotherapeutics appear to be driven by protein aggregates. Important factors in reducing antibody immunogenicity risk in the clinic are low t-cell epitope content, minimized non-human germline content and low aggregation potential.

Examples provided herein describe the “Augmented Binary Substitution” design principle that generates stable, soluble, ultra-humanized antibodies via single-step CDR redundancy minimization. For three antibodies from three separate key immune host species, binary substitution CDR cassettes were inserted into preferred human frameworks to form libraries in which only the donor (non-human) residue or human germline destination residue was encoded at each position. The CDR-H3 in each case was also augmented with 1±1 random substitution per clone. Each library was then screened for clones with restored antigen binding capacity. Lead ultra-humanized clones demonstrated high stability, with affinity and specificity equivalent to, or better than, the parental immunoglobulin. Significantly, this was mainly achieved on germline frameworks by simultaneously subtracting up to 19 redundant non-human residues in the CDRs. This significantly lowered non-human sequence content, minimized t and b-cell epitope risk in the final molecules and provided a heat map for desired non-human CDR residue content of each antibody.

Example 1: Library Design, Build and Characterization

Rat anti-RAGE XT-M4, rabbit anti-A33, and chicken anti-pTau pT231/pS235_1 IgGs were generated on the human IgG1 backbone with either parental (Par-RAGE, Par-A33 or Par-pTau), grafted (Graft-RAGE, Graft-A33 or Graft-pTau), or classically humanized (CL-Hum-RAGE, CL-Hum-A33) v-domains. In scFv format, the parental form of each of these antibodies retained antigen binding, while the human FW-grafted versions demonstrated little to no binding (FIGS. 5A-5C). ABS ultra-humanization libraries (ABS-RAGE, ABS-A33, ABS-pTau) were constructed (FIG. 1) to generate 1.8×10⁹ independent clones for ABS-RAGE, 1.1×10¹⁰ for ABS-A33 and 4.9×10⁹ for ABS-pTau (theoretical binary diversity for ABS-RAGE is 2²⁷ positions=1.34×10⁸, for ABS-A33 232=4.29×109 and for ABS-pTau 2³³=8.59×10⁹).

The quality of pTau library build was verified by sequence analyses of ≥96 clones/library. After library transformation, the full scFv insert sequences were obtained for 96 clones, via sanger sequencing. Positions mutated in the CDRs show the expected (approximately 50:50) variability at all positions expected to be sampled by binary substitutions and low-level mutagenesis in the CDR-H3, confirming the integrity of the sampled library. <1% of clones contained out of frame or truncated inserts. Libraries were rescued using helper phage M13 and selections performed on their cognate targets.

Example 2: Identification and Analysis of Ultra-Humanized Clones

Clone selection in ABS library screening (pTau example) was conducted. Periprep ELISA was conducted to screen for single clones picked from multiple rounds of phage display selections of the ABS-pTau library. One hundred and eighty-eight clones were prioritized on the basis of retention of binding to the pT231_pS253 phosphopeptide, with A450 readings above the negative control (Anti-RAGE scFv), and equivalent to or above that of Par-pTau scFv. Periprep HTRF was conducted to screen these 188 single clones for epitope competition with wild-type IgG. Clones were prioritized on the basis of neutralisation of Par-pTau IgG binding to the pT231_pS253 phosphopeptide, with % ΔF readings lower than the negative control (Anti-RAGE scFv) and equivalent to or better that of Par-pTau scFv.

Post-selection screening revealed the presence of numerous scFv clones with significantly increased human content within the CDRs. In the ABS-RAGE and ABS-A33 leads, the FW sequences remained fully germline. In the ABS-pTau leads, all selected clones retained the T46 back-mutation, illustrating that this VL-FW2 residue is desired to humanize chicken antibodies (FIGS. 6A-6B). Human germline amino acid content was quantified within the CDRs of parental antibodies and ABS leads and expressed as a percentage (Table 1). Human content had raised 17-29% in each case. From top to bottom, CDRL1: SEQ ID NOs. 278-290; CDRL2: SEQ ID NOs. 291-303; CDRL3: SEQ ID NOs. 304-316; CDRH1: SEQ ID NOs. 317-329; CDRH2: SEQ ID NOs. 330-342; CDRH3: SEQ ID NOs. 343-352.

Example 3: Lead IgG Affinity, Stability and Specificity Characteristics

ABS leads in human IgG1 format were analyzed for specificity and stability. HTRF data (FIGS. 7A-7C), showed that the lead ABS-derived IgGs had successfully maintained full epitope competition with their respective parental clones (Table 1). Biacore analyses showed approximately 2-fold affinity improvements for C7-ABS-RAGE and C21-ABS-pTau over Par-RAGE and Par-pTau, respectively, while C2-ABS-A33 maintained equivalent affinity to Par-A33 (Table 1).

A baculovirus ELISA assay (FIG. 8A) has been reported in antibody polyreactivity screening as a risk indicator for poor pK in vivo. In this assay, no reactivity was observed for any of the RAGE, A33 or pTau clones in comparison to an internal positive control antibody. For the anti-RAGE and anti-A33 antibodies, a high-sensitivity Biacore assay was also established, to examine the possibility that v-gene engineering might lead to low affinity interactions with multiple classes of proteins. A panel of 18 fully-purified, recombinant, non-target proteins was examined. This method showed that C7-ABS-RAGE and C2-ABS-A33 both maintained highly specific binding to their respective antigens (FIGS. 8B and 8C). For the anti-pTau antibodies, specificity for pT231/pS235 was confirmed using Biacore assays (FIG. 8D). All ABS-derived leads in this study were, therefore, absent of the ‘charge asymmetry’, lipophilicity, off-target protein binding or other problems that can arise during v-gene engineering.

DSC analysis of IgG thermal stabilities demonstrated that C7-ABS-RAGE, C2-ABS-A33 and C21-ABS-pTau were highly stable. C7-ABS-RAGE was particularly thermostable with a Fab Tm of 85° C.; similar to Graft-RAGE, but almost 8° C. higher than that of the CL-Hum-RAGE (FIG. 2A, Table 1). This is a finding of note, as it highlighted that the presence of back-mutations in CL-Hum-RAGE had significantly decreased the stability of the v-domains in comparison to the highly stable graft. C21-ABS-pTau exhibited a Fab Tm of 70° C., 4° C. higher than Graft-pTau (FIG. 2B). In forced aggregation analyses C7-ABS-RAGE, C21-ABS-pTau and C2-ABS-A33 all showed <1% aggregation at 60° C. (FIG. 2D, E, F, Table 1). Graft-pTau, in contrast, exhibited >90% aggregation at 60° C. Importantly, analysis of pH shock tolerance (which mimics virus-killing pH hold in mAb manufacturing) also showed each of the IgGs to be highly stable, with <3% loss observed.

Example 4: Human t and b-Cell Epitope Minimization in ABS Leads

ABS leads and associated precursors were examined for potential t-cell epitope content using the EpiMatrix software, generating a t-regitope adjusted score for each clone (FIG. 3A), as suggested in the recent draft FDA immunogenicity assessment guidelines. C7-ABS-RAGE, C2-ABS-A33 and C21-ABS-pTau showed scores of −53.72, −55.22 and −67.33 points, respectively. This lowered the projected immunogenicity of all clones into the same range as antibodies such as trastuzumab, which has been well tolerated in the clinic, and lower than ‘fully human’ antibodies such as adalimumab (FIG. 3A).

Analysis at the individual peptide level predicted that t-cell epitope content was clearly reduced for C7-ABS-RAGE and C21-ABS-pTau in comparison to their respective parental forms (FIG. 9). T-regitope content was also increased. Notably, the ratio of t-cell epitopes to t-regitopes was improved in C7-ABS-RAGE in comparison to CL-Hum-RAGE. Indeed, the removal of the back mutation found in the VL FW2 of CL-Hum-RAGE not only aided stabilization of the v-domains (FIG. 2A), but also removes a t-cell epitope and converts it into a germline t-regitope (FIG. 9). Analysis of the sequence of C21-ABS-pTau showed that the ABS-derived germlining at key positions in the CDR-H2 had ablated a foreign t-cell epitope at the N-terminus of the loop that had been introduced by CDR-grafting. Some potential epitopes of foreign sequence were still present however, even after ultra-humanization (FIG. 9). This reflects the need to retain certain key contact residues in the paratope and balance target recognition with t-cell epitopes and overall “humanness”. The L46T back mutation in C21-ABS-pTau was not predicted to introduce a t-cell epitope and this clone retained only a single predicted foreign t-cell epitope (in comparison to 5 in Par-pTau), driven by Q33 in the V_(H).

As a surrogate for b-cell epitope availability, non-human solvent-accessible surface area (nhSASA, measured in Å²) was calculated for the parental, graft and ABS lead clones. Clones C7-ABS-RAGE, C2-ABS-A33 and C21-ABS-pTau demonstrated minimized non-human surface area (FIG. 3B). C7-ABS-RAGE exhibited a reduction in nhSASA to 1077.6 Å², in comparison to the Par-RAGE and Graft-RAGE at 3084.8 and 1957.6, respectively. This represents a 45% reduction even in comparison to the Graft-RAGE. C21-ABS-pTau demonstrated a reduction to 1009.0 Å², in comparison to the Par-pTau and Graft-pTau at 3365.3 and 1372.1, respectively. C2-ABS-A33 showed a reduction to 1583.9 Å², in comparison to the Par-pTau and Graft-pTau at 4260.7 and 2240.2, respectively (FIG. 3B).

Further analyses were performed using publically available software, to numerically define the overall levels of human repertoire identity of the parental and ABS-derived leads, in comparison with 33 antibodies currently approved as therapeutics with murine, humanized or “fully human” v-domains. These analyses showed that the ABS clones had distinctly improved T20, G and Z scores over parental clones. Indeed, the C7-ABS-RAGE clone had scores placing it in the range of values found for the ‘fully human’ antibody group, with the C2-ABS-A33 and C21-ABS-pTau clones close behind (FIG. 3C).

Example 5: Strongly Maintained Non-Human CDR Content Via Mutational Tolerance and Structural Analyses

The screening of output clones from the ABS-pTau library identified 188 sequence-unique hits with binding signals ≥the parental scFv (data not shown). For residues targeted in the library for binary substitution, positional amino acid usage frequencies were calculated for these hits and expressed as a percentage (FIGS. 4A-4B). Amino acid positions with parental residue usage frequencies of >75% were labeled “strongly maintained” (SM), i.e. with the chicken residue being positively selected. Those with frequencies below 25% were labeled “strongly deleted” (SD), i.e. the human germline residue being preferred.

Heatmaps of non-human residue content in the anti-pTau binding site for Par-pTau, Graft-pTau and C8-ABS-pTau were also generated (data not shown). The heatmaps show that the ABS process better defines residues that may be important for antigen-binding function.

When the SM residues were compared with those previously predicted to be key contacts via a co-crystal structure, the two populations were found to clearly overlap. Across both chains, however, SM positions were found to be only 29.6% (17/55) of the total CDR residues outside the CDR-H3. In the V_(H) domain, Q33, T52, S53, R54 were all predicted contact residues and all were SM, with retention frequencies >90%. G55 and G56 were also predicted to be key contacts but were not sampled in the library, as they were fully conserved human to chicken. Interestingly, the S53G substitution, while not heavily favored in the selected population, could clearly be functional, as seen in the C21-ABS-pTau clone, so long as T52, R54, G55 and G56 were maintained (FIG. 6). Other SM residues in the V_(H) were found to be contact-proximal and/or desirable for appropriate presentation of the contact residues, such as M35, A49, G50, V57 and G59.

Of 4 predicted contact residues in the V_(L), only Y91 was found to be SM and was retained at 100%. Other SM residues were predominantly found in stem-loop positions of CDR-L3 (G89, G96, G98) and CDR-L1 (G34), which may be influential on loop structure. Additionally, the SM N51 site forms structurally supportive hydrogen bonds between the CDR-L1 and V_(L) FW2.

Out of 33 residues sampled by binary substitution, only a single SD residue (V_(H)L29) was identified, suggesting that all 16 other non-SM residues were interchangeable. On the basis of these analyses, we interpreted the “strongly non-human CDR content”, meaning those parental residues that are unlikely be germlined, even if compensated by the mutation of a residue elsewhere in the paratope (FIGS. 4A-4B). This also informed the minimization of chicken residue content by making a combination clone, Combo-ABS-pTau. This clone contains the most “human” variant of each CDR that had been observed in the top ABS-pTau hits (FIG. 6, Table 1). This reduced non-human content by another 6 residues versus C21-ABS-pTau, pushing the Combo-ABS-pTau to 76% human in the CDRs, but adding one more predicted t-cell epitope than C21-ABS-pTau (FIG. 9). The retained non-human residues in Combo-ABS-pTau closely matched to the SM set of residues described above (FIGS. 4A-4B). Combo-ABS-pTau was found to be soluble, stable and maintained the binding affinity and specificity of Par-pTau (Table 1, FIG. 2A).

Example 6: Additional CDR-Humanized Antibodies

The sequences of additional CDR-humanized antibodies are shown in Tables 7-12. CDR sequences are in bold. Donor v-genes (murine, rat, rabbit, or chicken) and human germline DP/J designations are included. CDR residues from the parent clone that differ from human germline are underlined.

Summary

Despite considerable investigation, current antibody humanization methods often create therapeutic molecules with significant risk factors for the failure of a lead drug due to potential immunogenicity and/or poor pK in the clinic, or because the molecule cannot be manufactured and delivered in a cost-effective manner. These risks are potentially exacerbated if the lead is derived from hosts such as rats, rabbits or chickens, rather than the heavily characterized antibody repertoires of mice and humans.

Antibodies from alternative immune species can provide excellent IgGs with unique functional characteristics against problematic targets (e.g. highly conserved across species), but their antibodies are also known to exhibit unique sequence/structural features. These antibodies therefore require maximal humanization and development validation if they are to gain broad acceptance as potential clinical leads. Indeed, despite their therapeutic potential, there are currently no chicken antibodies and only one known humanized rabbit antibody in the clinic. In establishing the ABS technology we have shown that it is possible to minimize clinical and manufacturing concerns, by making antibodies from all 3 sources stable, soluble and of low immunogenicity risk. When analyzed in silico, human identity and t-cell epitope risk appeared to be indivisible between C7-ABS-RAGE and currently marketed ‘fully human’ antibodies, with C21-ABS-pTau and C2-ABS-A33 comparable to the best of the humanized mouse antibodies currently approved for clinical use.

Other humanization methods do not factor in the CDRs themselves as mediators of stability and solubility, in addition to the frameworks. Antibodies from species with limited starting framework diversity in both the V_(H) and V_(L) genes fit the ABS technology particularly well. Indeed, chickens and rabbits use V_(H) repertoires that are highly homologous to human V_(H)3 domain. For murine antibodies, FW diversity in the functional repertoire is much higher than for chickens or rabbits. Prior estimations of v-domain homology, pairing angle and V_(H)-V_(L) packing are therefore prudent, to aid the prediction of whether preferred germlines.

Previous methods that maintain the animal CDR-H3 (+/−CDR-L3), then sample human repertoire diversity to return binding affinity, may suffer from an inability to recapitulate the critical structural characteristics found outside the CDR-H3s of non-murine antibodies, as exemplified by our anti-pTau mAb. These methods also frequently leave, or generate, significant numbers of framework mutations away from germline which can lower the stability of v-domains. Indeed, the C7-ABS-RAGE clone illustrated that the CDRs from XT-M4 could be heavily germlined and the back mutations from classical humanization fully removed, greatly improving stability in the final molecule.

This study illustrates that 3 separate antibodies from 3 species, targeting 3 different epitopes, all have high levels of sequence redundancy in their paratopes that can be exploited for v-domain risk reduction engineering without the need for prior structural analyses. The retention of SM residues in the CDRs of selected clones after ABS strongly correlated with the prediction of key contact residues in the co-crystal structure of anti-pTau with its target antigen. Residues were also found to be SM if they were likely to be desirable for the correct presentation of CDR loops. In only one case was a framework back mutation necessary to include during humanization (V_(L) L46T, anti-pTau). This suggests that many of the back mutations required during classical humanization of anti-RAGE and anti-A33 were likely necessitated by the retention of non-human CDR residues that clash with human framework residue side chains, but are functionally redundant in antigen binding. ABS intrinsically minimized redundant animal-derived CDR content by selecting for the retention of essential non-human residues and allowing the rest of the CDR to be converted to the sequence of the destination v-gene. This approach thereby simultaneously optimized all functional parameters of these three potential therapeutic antibodies, which were derived from species often used in monoclonal antibody generation against challenging therapeutic targets.

Materials and Methods for Examples 1-6

ScFv-based library designs. Parental and CDR-grafted forms of rat Anti-RAGE, rabbit anti-A33 and chicken anti-pTau antibodies, plus a classically humanized (CL-Hum) version of XT-M4 were synthesized (Geneart™) in V_(L)-V_(H) scFv format, ligated into the phagemid pWRIL-1 and cloned into E. coli TG1 cells. Soluble periplasmic E. coli expression was confirmed by SDS-PAGE and western blot. Function of each construct was assessed via direct binding ELISA (as purified scFv or periprep). Based on these scFv constructs, Augmented Binary Substitution libraries were designed in silico (FIG. 1) and synthesized as finished dsDNA scFv fragments (Geneart™). Anti-pTau is a Type 1 chicken IgG with critical secondary structural characteristics in CDR H2 and H3, and a recent structural study of a humanized chicken antibody suggested that a back mutation at V_(λ) FW2 position 46 (L46T) is critical to the correct packing of the V_(λ) against the CDR-H3 stem-loopTo examine whether or not this was still true when random point mutations are also being simultaneously sampled in the CDR-H3, a binary substitution (L/T) was allowed at VA position 46 in the ABS-pTau library.

Construction, Selection and Screening of scFv Libraries.

The ABS scFv libraries were constructed rescued and selected. Solution phase selection on biotinylated target antigen with streptavidin beads was employed throughout. Post-selection ELISA and HTRF screening, epitope competition analyses and reformatting were performed. For details, see Finlay, W. J. et al. J Mol Biol 388, 541-558 (2009).

IgG Expression and Biophysical Analyses.

IgGs were transiently expressed in HEK-293f cells after transfection with IgG expression plasmids and lipofectamine 2000 (Invitrogen), according to manufacturer's protocols. Automated purification was carried out using ProPlus resin tips on the MEA system (Phynexus). Differential Scanning Calorimetry, Forced Aggregation and pH stability analyses were performed according to King, A. C. et al. Protein Sci 20, 1546-1557 (2011).

Biacore Analysis of Binding Kinetics.

Biacore analysis was performed using the T-200 biosensor, series S CM5 chips, an amine-coupling kit, 10 mM sodium acetate immobilization buffer at pH 5.0, 10×HBS-P running buffer and NaOH for regeneration (GE Healthcare). Kinetic assay conditions were established to minimize the influence of mass transfer, avidity and rebinding events. A predefined ligand immobilization program was set up to immobilize approximately 100 Response Units (RU) of IgG on the chip. Purified target proteins were diluted in HBS-P running buffer to a range of final concentrations and injected at 50 μl/min for 3 mins. Dissociation was allowed to proceed for 10 min followed by a 5 sec pulse of 20 mM NaOH for regeneration of the chip surface. All sensorgrams were analyzed using the Biacore T-200 evaluation software.

Binding Specificity Analyses.

Anti-RAGE, pTau and A33 antibodies were tested for polyreactivity by ELISA and Biacore analyses. ELISAs were performed against single stranded DNA, double stranded DNA, insulin and lipopolysaccaride, and against Baculovirus particles All polyreactivity analyses used parental antibodies and Pfizer in-house positive and negative control antibodies.

Biacore specificity analyses were performed using the T-200 biosensor, series S CM5 chips, an amine-coupling kit, 10 mM sodium acetate immobilization buffer at pH 5.0, 10×HBS-P running buffer and NaOH for regeneration (GE Healthcare). A predefined ligand (IgG) immobilization program was set up to immobilize approximately 300 Response Units (RU) on the flow cell for each IgG to be tested. For Anti-RAGE and anti-A33, a panel of fully-purified recombinant target and non-target antigens were diluted in HBS-P running buffer to a final concentration of 500 nM. Four groups of antigens were examined, including: cell membrane proteins (mTRKB, hTRKB, mEGFR, hEGFR, hFceR1, hIL-21R, mICAM1, mICAM2, hICAM1, hCD33, hLAMP-1, hLOX-1, and), soluble signaling molecules (mTNFa, hVEGF, hCXCL13) and albumins (BSA, HSA and MSA). These proteins were injected at 50 μl/min for 3 min, followed by a 5 sec pulse of 20 mM NaOH for regeneration of the chip surface. For pTau, a series of pTau-derived phosphorylated and non-phosphorylated peptides were flowed, as in Shih et al.³. All sensorgrams were analyzed using the Biacore T-200 evaluation software.

Modeling Analyses.

Variable domain structural models were generated for the parental, humanized and ABS humanized variants of the anti-pTAU and the anti-RAGE antibodies. The Protein Databank (PDB) crystal structure 4GLR of the anti-pTau antibody was used for the parental pTau model. For the humanized and ABS humanized pTau antibodies, we generated homology models using Modeller version 9.12 with the PDB structures of 4GLR and 3G6A as templates. For all three XTM4 structures, homology models were also generated using Modeller with template structure 1fvd, 1dql, 3hns, 1mhp, 1bbj, 1bog, 1aif, 1arl and 1rmf for the parental; 1fvd, 1dql, 1mhp, 3hns, 1bbj, 1bog, 1aif, 1arl and 1 rmf for the humanized; and 1mhp, 3hns, 2cmr, 1gig, 2ghw, 1aif and 1rmf for the ABS humanized. The non-human solvent accessible surface area (nhSASA) was calculated using the “Solvent Accessibility” calculator in the molecular modeling software suite Discovery Studio Client 4.0 (Accelrys Inc). The nhSASA was defined as the sum of the side-chain SASA of residues that were not identical to germline.

In Silico t-Cel Epitope Assessment.

Sequences of antibody V_(H) and V_(L) regions were analyzed by EpiMatrix (Epivax, RI) Briefly, each domain was parsed into overlapping 9-mer peptides with each peptide overlapping the last by eight amino acids. Each peptide was then scored for predicted binding to each of eight HLA Class II alleles (DRB1*0101, DRB1*0301, DRB1*0401, DRB1*0701, DRB1*0801, DRB1*1101, DRB1*1301, and DRB1*1501) which represent HLA supertypes covering 97% of human populations worldwide. Any peptide scoring above 1.64 on the EpiMatrix “Z” scale (approximately the top 5% of the random peptide set) was classed as a “hit” for binding to the MHC molecule for which it was predicted. Peptides scoring four or more hits from the eight alleles predicted are considered as possible epitopes. Some germ-line sequences have been suggested to induce t regulatory cells. A previous study with a therapeutic protein demonstrated a correlation between an immunologically active peptide, i.e. t-cell epitope, and the EpiMatrix prediction (Koren, E. et al. Clin Immunol 124, 26-32 (2007)).

The various features and embodiments of the present invention, referred to in individual sections above apply, as appropriate, to other sections, mutatis mutandis. Consequently features specified in one section may be combined with features specified in other sections, as appropriate.

All references cited herein, including patents, patent applications, papers, text books, and the like, and the references cited therein, to the extent that they are not already, are hereby incorporated by reference in their entirety. In the event that one or more of the incorporated literature and similar materials differs from or contradicts this application, including but not limited to defined terms, term usage, described techniques, or the like, this application controls.

TABLE 1 CDR sequence, affinity and stability characteristics of parental, grafted and  ABS-derived lead clones. % germ- line # FW in muta- CDRL1* CDRL2 CDRL3 CDRH1 CDRH2 CDRH3 CDRs tions DPK9/ RASQSISSYLN AASSLQS QQSYSTPLT GFTFSSYWMS ANIKQDGSEKYYVDSVKG n/a 100 n/a DP54 germ- lines CL- RASQDVGIYVN RATNLAD LEFDEHPLT GFTFSNYWMT ASIDNSGDNTYYPDSVKD GGDITTGFDY 45 5 Hum- RAGE Graft- RASQDVGIYVN RATNLAD LEFDEHPLT GFTFSNYWMT ASIDNSGDNTYYPDSVKD GGDITTGFDY 45 0 RAGE C7- RASQSIGSYLN RASSLAS LEFDEHPLT GFTFSSYWMS ASIDQDGSNKYYPDSVKG GGDITTGLDY 74 0 ABS- RAGE DPK9/ RASQSISSYLN AASSLQS QQSYS--TPLT GFTFSSYAMS SAISGSGGSTYYADSVKG n/a 100 n/a DP47 germ- lines Chim- LASEFLFNGVS GASNLES LGGYSGSSGLT GIDFSHYGIS AYIYPNYGSVDYASWVNG DRGYYSGSRGTRLDL 39 n/a A33 Graft- LASEFLFNGVS GASNLES LGGYSGSSGLT GIDFSHYGIS SYIYPNYGSVDYASWVNG DRGYYSGSRGTRLDL 39 0 A33 C6- RASQFLFNGVS AASNLES QGGYSGSTGLT GFTFSHYGIS SYIYPSYGSTDYASSVKG DRGYYSGSRGTRLDL 56 0 ABS- A33 DPL16/ QGDSLRSYYAS GKNNRPS NSRDSSGNHVV GFTFSSYAMS SAISGSGGSTYYADSVKG n/a 100 n/a DP47 germ- lines Chim- SGSD--YDYG- WNDKRPS GAYDGSAGGGI GFTLSSYQMM AGITSRGGVTGYGSAVKG PALDSDQCGFPEA- 41 n/a pTau GCIDA Graft- SGSD--YDYG- WNDKRPS GAYDGSAGGGI GFTLSSYQMM AGITSRGGVTGYGSAVKG PALDSDQCGFPEA- 41 0 ABS- GCIDA pTau C21- QGDD--SYYG- GNDNRPS GAYDSSGGGGI GFTLSSYQMM AGITGRGGVTGYADSVKG PALDSDQCGFPEA- 65 1 ABS- GCIDA pTau Com- QGDD--SYYG- GNNNRPS GSYDSSGGHGV GFTFSSYQMS SGITGRGGVTGYADSVKG PALDSDQCGFPEM- 76 1 ABS- GCIDA pTau From  SEQ ID SEQ ID  SEQ ID SEQ ID  SEQ ID SEQ ID NOs:  top  NOs:  NOs:  NOs:  NOs:  NOs:  343-352 to  278-290 291-303 304-316 317-329 330-342 bot- tom: IC50 kD (nM) (nM) Tm HTRF SPR % Agg 60° C. (° C.) % Agg pH shock DPK9/DP54  n/a n/a n/a n/a n/a germlines CL-Hum-RAGE 10.3 31.0 14 77 3.2 Graft-RAGE >61.9 ND 0 84 1.8 C7-ABS-RAGE 5.8 17.0 0 85 2.1 DPK9/DP47  n/a n/a n/a n/a n/a germlines Chim-A33 2.9 2.1 0 74 1.5 Graft-A33 ND ND ND ND ND C6-ABS-A33 2.7 2.1 0 74 0.4 DPL16/DP47 n/a n/a n/a n/a n/a germlines Chim-pTau 1.6 0.41 17 70 1.2 Graft-ABS- >64.7 NB 90 66 0.8 pTau C21-ABS- 2.1 0.25 3 70 1.2 pTau Com-ABS- ND 0.50 2 71 1.4 pTau *The pTau CDR-L1 is shorter than its DPL16 counterpart by 3 amino acids. Sequence dashes in this CDR are added to show the spacing of sampled residues. Residues differing from human germline are underlined.

TABLE 2 Exemplary Human V_(H )germline sequences Human VH1 germline sequence (from top to bottom, SEQ ID NOs. 56-69). VH1 FW1 CDR1 FW2 CDR2 FW3 IGHV1-2 QVQLVQSGAEVKKPGASVKVSCKAS GYTFTGYYMH.. WVRQAPGQGLEWM GRINP..NSGGTNYAQKFQG RVTSTRDTSISTAYMELS RLRSDDTVVYYCAR. IGHV1-3 QVQLVQSGAEVKKPGASVKVSCKAS GYTFTSYAMH.. WVRQAPGQRLEWM GWINA..GNGNTKYSQKFQG RVTITRDTSASTAYMELS SLRSEDIAVYYCAR. IGHV1-8 QVQLVQSGAEVKKPGASVKVSCKAS GYTFTSYDIN.. WVRQATGQGLEWM GWMNP..NSGNTGYAQKFQG RVTMTRNTSTSTAYMELS SLRSEDTAVYYCAR. IGHV1-18 QVQLVQSGAEVKKPGASVKVSCKAS GYTFTSYGIS.. WVRQAPGQGLEWM GWISA..YNGNTNYAQKLOG RVTMTTDTSTSTAYMELR SLRSDDTAVYYCAR. IGHV1-24 QVQLVQSGAEVKKPGASVKVSCKVS GYTLTELSMH.. WVRQAPGKGLEWM GGFDP..EDGETIYAQKFOG RVTMTEDTSTDTAYMELS SLRSEDTAVYYCAT. IGHV1-38-4 QVQLVQSWAEVRKSGASVKVSCSFS GFTITSYGIH.. WVQQSPGQGLEWM GWINP..GNGSPSYAKKFQG RFTMTRDMSTITAYTDLS SLTSEDMAVYYYAR. IGHV1-45 QMQLVQSGAEVKKTGSSVKVSCKAS GYTFTYRYLH.. WVRQAPGQALEWM GWITP..FNGNTNYAQKFQD RVTITRDRSMSTAYMELS SLRSEDTAMYYCAR. IGHV1-46 QVQLVQSGAEVKKPGASVKVSCKAS GYTFTSYYMH.. WVRQAPGQALEWM GIINP..SGGSTSYAQKFQG RVTMTRDISTSTVYMELS SLRSEDTAVYYCAR. IGHV1-58 QMQLVQSGPEVKKPGTSVKVSCKAS GFTFTSSAVQ.. WVRQARGQRLEWI GWIVV..GSGNTNYAQKFQE RVTITRDMSTSTAYMELS SLRSEDTAVYYCAA. IGHV1-68 QVQLGQSEAEVKKPGASVKVSCKAS GYTFTCCSLH.. WLQQAPGQGLERM RWITL..YNGNTNYAKKFQG RVTITRDMSLRTAYIELS SLRSEDSAVYYWAR. IGHV1-68-2 EVQLVQSGAEVKKPGATVKISCKVS GYTFTDYYMH.. WVQQAPGKGLEWM GLVDP..EDGETIYAEKFQG RVTITADTSTDTAYMELS SLRSEDTAVYYCAT. IGHV1-69 QVQLVQSGAEVKKPGSSVKVSCKAS GGTFSSYAIS.. WVRQAPGQGLEWM GGIIP..IFGTANYAQKFQG RVTITADESTSTAYMELS SLRSEDTAVYYCAR. IGHV1-69D QVQLVQSGAEVKKPGSSVKVSCKAS GGTFSSYAIS.. WVRQAPGQGLEWM GGIIP..IFGTANYAQKFQG RVTITADESTSTAYMELS SLRSEDTAVYYCAR. IGHV1-NL1 QVQLLQPGVQVKKPGSSVKVSC*AS RYTFTKYFTR.. WV*QSPGQGHXWM G*INP..YNDNTHYAQTFWG RVTITSDRSMSTAYMELS XLRSEDMVVYYCVR. Human VH2 germline sequence (from top to bottom, SEQ ID NOs. 70-73). VH2 FW1 CDR1 FW2 CDR2 FW3 IGHV2-5 QITLKESGPTLVKPTQTLTLTCTFS GFSLSTSGVGVG WIRQPPGKALEWL ALIY...WNDDKRYSPSLKS RLTITKDISKNQVVLTMT NMDFVDTATYYCAHR IGHV2-10 QVTLKESGPALVKPTQTLMLTCTFS GFSLSTSGMGVG *ICQPSAKALEWL AHIY...*NDNKYYSPSLKS RLIISKDTSKNEVVLTVI NMDIVDTATHYCARR IGHV2-26 QVTLKESGPVLVKPTETLTLTCTVS GFSLSNARMGVG WIRQPPGKALEWL AHIF...SNDEKSYSTSLKS RLTISKDTSKSQVVLTMT NMDPVDTATYYCARI IGHV2-70 QVTLRESGPALVKPTQTLTLTCTFS GFSLSTSGMCVS WIRQPPGKALEWL ALID...WDDSKYYSTSLKT RLTISKDTSKNQVVLTMT NMDPVDTATYYCARI Human VH3 germline sequence (from top to bottom, SEQ ID NOs: 74-114): VH3 FW1 CDR1 FW2 CDR2 FW3 IGHV3-7 EVQLVESGGGLVQPGGSLRLSCAAS GFTFSSYWMS.. WVRQAPGKGLEWV ANIKQ..DGSEKYYVDSVKG RFTISRDNAKNSLYLQMN SLRAEDTAVYYCAR. IGHV3-9 EVQLVESGGGLVQPGRSLRLSCAAS GFTFDDYAMH.. WVRQAPGKGLEWV SGISN..NSGSIGYADSVKG RFTISRDNAKNSLYLQMN SLRAEDTALYYCAKD IGHV3-11 QVQLVESGGGLVKPGGSLRLSCAAS GFTFSDYYMS.. WIRQAPGKGLEWV SYISS..SGSTIYYADSVKG RFTISRDNAKNSLYLQMN SLRAEDTAVYYCAR. IGHV3-13 EVQLVESGGGLVQPGGSLRLSCAAS GFTFSSYDMH.. WVRQAIGKGLEWV SAIG...TAGDTYYPGSVKG RFTISRENAKNSLYLQMN SLRAGDTAVYYCAR. IGHV3-15 EVQLVESGGGLVKPGGSLRLSCAAS GFTFSNAWMS.. WVRQAPGKGLEWV GRIKSKTDGGTTDYAAPVKG RFTISRDDSKNTLYLQMN SLKTEDTAVYYCTT. IGHV3-16 EVQLVESGGGLVQPGGSLRLSCAAS GFTFSNSDMN.. WARKAPGKGLEWV SGVSW..NGSRTHYVDSVKR RFTISRDNSRNSLYLQKN RRRAEDMAVYYCVR. IGHV3-19 TVQLVESGGGLVEPGGSLRLSCAAS GFTFSNSDMN.. WVRQAPGKGLEWV SGVSW..NGSRTHYADSVKG RFTISRDNSRNFYLQQMN SLRPEDMAVYYCVR. IGHV3-20 EVQLVESGGGLVRPGGSLRLSCAAS GFTFDDYGMS.. WVRQAPGKGLEWV SGINW..NGGSTGYADSVKG RFTISRDNAKNSLYLQMN SLRAEDTALYHCAR. IGHV3-21 EVQLVESGGGLVKPGGSLRLSCAAS GFTFSSYSMN.. WVRQAPGKGLEWV SSISS..SSSYIYYADSVKG RFTISRDNAKNSLYLQMN SLRAEDTAVYYCAR. IGHV3-22 EVHLVESGGALVQPGGSLRLSCAAS GFTFSYYYMS.. GVRQAPGKGLEWV GFIRNKANGGTTE*TTSVKG RFTISRDDSKSITYLQMK SLKTEDTAVYYCAR. IGHV3-23 EVQLLESGGGLVQPGGSLRLSCAAS GFTFSSYAMS.. WVRQAPGKGLEWV SAISG..SGGSTYYADSVKG RFTISRDNSKNTLYLQMN SLRAEDTAVYYCAK. IGHV3-23D EVQLLESGGGLVQPGGSLRLSCAAS GFTFSSYAMS.. WVRQAPGKGLEWV SAISG..SGGSTYYADSVKG RFTISRDNSKNTLYLQMN SLRAEDTAVYYCAK. IGHV3-25 EMQLVESGGGLQKPAWSPRLSCAAS QFTFSSYYMN.. CVRQAPGNGLELV *QVNP..NGGSTYLIDSGKD RFNTSRDNARNTLHLQMN SLKTEDTALY*CTR. IGHV3-29 EVELIEPTEDLRQPGKFLRLSCVAS RFAFSSF*MS.. PVHQSAGKGLE*V IDIKD..DGSQIHHADSVKG RFSISKDNAKNSLYLQMN SQRTEDMAVYGCT*G IGHV3-30-2 EVQLVESGEDPRQPGGSLRLSCADS GLTFSSY*RN.. SVSQAPGKGLE*V VDIQC..DGSQICYA*SLKS KFTISKENAKNSLYLLMN SLRAAGTAVCYCM*G IGHV3-30-3 QVQLVESGGGVVQPGRSLRLSCAAS GFTFSSYAMH.. WVRQAPGKGLEWV AVISY..DGSNKYYADSVKG RFTISRDNSKNTLYLQMN SLRAEDTAVYYCAR. IGHV3-30 QVQLVESGGGVVQPGRSLRLSCAAS GFTFSSYAMH.. WVRQAPGKGLEWV AVISY..DGSNKYYADSVKG RFTISRDNSKNTLYLQMN SLRAEDTAVYYCAR. IGHV3-32 EVELIESIEDLRQPGKFLRLSCVAS RFAFSSF*MS.. RVHQSPGKGLE*V IDIKD..DGSQIHHADSVKG RFSISKDNAKNSLYLQMN TQRAEDVAVYGYT*G IGHV3-33-2 EVQLVESGEDPRQPGGSLRLSCADS GLTFSSY*MS.. SVSQAPGKGLE*V VDIQC..DGSQICYAQSVKG KFTISKENAKNSLYLQMN SLRAEGTAVCYCM*G IGHV3-33 QVQLVESGGGVVQPGRSLRLSCAAS GFTFSSYGMH.. WVRQAPGKGLEWV AVIWY..DGSNKYYADSVKG RFTISRDNSKNTLYLQMN SLRAEDTAVYYCAR. IGHV3-35 EVQLVESGGGLVQPGGSLRLSCAAS GFTFSNSDMN.. WVHQAPGKGLEWV SGVSW..NGSRTHYADSVKG RFTISRDNSRNTLYLQTN SLRAEDTAVYYCVR. IGHV3-38-3 EVQLVESRGVLVQPGGSLRLSCAAS GFTVSSNEMS.. WVRQAPGKGLEWV SSIS....GGSTYYADSRKG RFTISRDNSKNTLHLQMN SLRAEDTAVYYCKK. IGHV3-38 EVQLVESGGGLVQPRGSLRLSCAAS GFTVSSNEMS.. WIRQAPGKGLEWV SSIS....GGSTYYADSRKG RFTISRDNSKNTLYLQMN NLRAEGTAAYYCARY IGHV3-43 EVQLVESGGVVVQPGGSLRLSCAAS GFTFDDYTMH.. WVRQAPGKGLEWV SLISW..DGGSTYYADSVKG RFTISRDNSKNSLYLQMN SLRTEDTALYYCAKD IGHV3-43D EVQLVESGGVVVQPGGSLRLSCAAS GFTFDDYAMH.. WVRQAPGKGLEWV SLISW..DGGSTYYADSVKG RFTISRDNSKNSLYLQMN SLRAEDTALYYCAKD IGHV3-47 EVQLVESGGGLVQPGGSLRPSCAAS GFAFSSYALH.. WVRRAPGKGLEWV SAIG...TGGDTYYADSVMG RFTISRDNAKKSLYLHMN SLIAEDMAVYYCAR. IGHV3-48 EVQLVESGGGLVQPGGSLRLSCAAS GFTFSSYSMN.. WVRQAPGKGLEWV SYISS..SSSTIYYADSVKG RFTISRDNAKNSLYLQMN SLRAEDTAVYYCAR. IGHV3-49 EVQLVESGGGLVQPGGSLRLSCTAS GFTFGDYAMS.. WFRQAPGKGLEWV GFIRSKAYGGTTEYTASVKG RFTISRDGSKSIAYLQMN SLKTEDTAVYYCTR. IGHV3-52 EVQLVESG*GLVQPGGSLRLSCAAS GFTFSSSWMH.. WVCQAPEKGLEWV ADIKC..DGSEKYYVDSVKG RLTISRDNAKNSLYLQVN SLRAEDMTVYYCVR. IGHV3-53 EVQLVESGGGLIQPGGSLRLSCAAS GFTVSSNYMS.. WVRQAPGKGLEWV SVIY...SGGSTYYADSVKG RFTISRDNSKNTLYLQMN SLRAEDTAVYYCAR. IGHV3-54 EVQLVESERNQRQLGGSLRLSCADS GLTFSSY*MS.. SDSQAPGKGLE*V VDI**..DRSQLCYAQSVKS RFTISKENAKNSLCLQMN SLRAEGTAVYYCM*. IGHV3-62 EVQLVESGEGLVQPGGSLRLSCAAS GFTFSSSAMH.. WVRQAPRKGL*WV SVIST..SGDTVLYTDSVKG RFTISRDNAQNSLSLQMN SLRAEGTVVYYCVK. IGHV3-63 EVELIESIEGLRQLGKFLRLSCVAS GFTFSSY*MS.. WVNETLGKGLEGV IDVKY..DGSQIYHADSVKG RFTISKDNAKNSPYLQVN SLRAEDMTMHGCT*G IGHV3-64 EVQLVESGGGLVQPGGSLRLSCAAS GFTFSSYAMH.. WVRQAPGKGLEYV SAISS..NGGSTYYANSVKG RFTISRDNSKNTLYLQMG SLRAEDMAVYYCAR. IGHV3-65 EVQLVESGGGLVQPGGSLRLSCAAS GFTVSSNYMS.. WVRQAPGKGLEWV SVIY...SGGSTYYADSVKG RFTISRDNSKNTLYLQMN SLRAEDTAVYYCAR. IGHV3-69-1 EVQLVESGGGLVKPGGSLRLSCAAS GFTFSDYYMN.. WVRQAPGKGLEWV SSIS..SSSTIYYADSVKG RFTISRDNAKNSLYLQMN SLRAEDTAVYYCAR. IGHV3-71 EVQLVESGGGLVQPGGSLRLSCAAS GFTFSDYYMS.. WVRQAPGKGLEWV GFIRNKANGGTTE*TTSVKG RFTISRDDSKSITYLQMN SLRAEDTAVYYCAR. IGHV3-72 EVQLVESGGGLVQPGGSLRLSCAAS GFTFSDHYMD.. WVRQAPGKGLEWV GRIRNKANSYTTEYAASVKG RFTISRDDSKNSLYLQMN SLKTEDTAVYYCAR. IGHV3-73 EVQLVESGGGLVQPGGSLKLSCAAS GFTFSGSAMH.. WVRQASGKGLEWV GRIRSKANSYATAYAASVKG RFTISRDDSKNTAYLQMN SLKTEDTAVYYCTR. IGHV3-74 EVQLVESGGGLVQPGGSLRLSCAAS GFTFSSYWMH.. WVRQAPGKGLVWV SRINS..DGSSTSYADSVKG RFTISRDNAKNTLYLQMN SLRAEDTAVYYCAR. IGHV3-NL1 QVQLVESGGGVVQPGGSLRLSCAAS GFTFSSYGMH.. WVRQAPGKGLEWV EVIYS..GGSSTYYADSVKG RFTISRDNSKNTLYLQMN SLRAEDTAVYYCAK. Human VH4 germline sequence (from top to bottom, SEQ ID NOs. 115-125): VH4 FW1 CDR1 FW2 CDR2 FW3 IGHV4-4 QVQLQESGPGLVKPPGTLSLTCAVS GGSISSSNWWS. WVRQPPGKGLEWI GEIY...HSGSTNYNPSLKS RVTISVDKSKNQFSLKLS SVTAADTAVYCCAR. IGHV4-28 QVQLQESGPGLVKPPDTLSLTCAVS GYSISSSNWWG. WIRQPPGKGLEWI GYIY...YSGSTYYNPSLKS RVTMSVDTSKNQFSLKLS SVTAVDTAVYYCAR. IGHV4-30-2 QLQLQESGSGLVKPSQTLSLTCAVS GGSISSGGYSWS WIRQPPGKGLEWI GYIY...HSGSTYYNPSLKS RVTISVDRSKNQFSLKLS SVTAADTAVYYCAR. IGHV4-30-4 QVQLQESGPGLVKPSQTLSLTCTVS GGSISSGDYYWS WIRQPPGKGLEWI GYIY...YSGSTYYNPSLKS RVTISVDTSKNQFSLKLS SVTAADTAVYYCAR. IGHV4-31 QVQLQESGPGLVKPSQTLSLTCTVS GGSISSGGYYWS WIRQHPGKGLEWI GYIY...YSGSTYYNPSLKS LVTISVDTSKNQFSLKLS SVTAADTAVYYCAR. IGHV4-34 QVQLQQWGAGLLKPSETLSLTCAVY GGSFSGYYWS.. WIRQPPGKGLEWI GEIN...HSGSTNYNPSLKS RVTISVDTSKNQFSLKLS SVTAADTAVYYCAR. IGHV4-38-2 QVQLQESGPGLVKPSETLSLTCAVS GYSISSGYYWG. WIRQPPGKGLEWI GSIY...HSGSTYYNPSLKS RVTISVDTSKNQFSLKLS SVTAADTAVYYCAR. IGHV4-39 QLQLQESGPGLVKPSETLSLTCTVS GGSISSSSYYWG WIRQPPGKGLEWI GSIY...YSGSTYYNPSLKS RVTISVDTSKNQFSLKLS SVTAADTAVYYCAR. IGHV4-55 QVQLQESGPGLVKPSETLSLTCAVS GDSISSGNW*I. WVRQPPGKGLEWI GEIH...HSGSTYYNPSLKS RITMSVDTSKNQFYLKLS SVTAADTAVYYCAR. IGHV4-59 QVQLQESGPGLVKPSETLSLTCTVS GGSISSYYWS.. WIRQPPGKGLEWI GYIY...YSGSTNYNPSLKS RVTISVDTSKNQFSLKLS SVTAADTAVYYCAR. IGHV4-61 QVQLQESGPGLVKPSETLSLTCTVS GGSVSSGSYYWS WIRQPPGKGLEWI GYIY...YSGSTNYNPSLKS RVTISVDTSKNQFSLKLS SVTAADTAVYYCAR. Human VH5 germline sequence (from top to bottom, SEQ ID NOs. 126-128): VH5 FW1 CDR1 FW2 CDR2 FW3 IGHV5-10-1 EVQLVQSGAEVKKPGESLRISCKGS GYSFTSYWIS.. WVRQMPGKGLEWM GRIDP..SDSYTNYSPSFQG HVTISADKSISTAYLQWS SLKASDTAMYYCAR. IGHV5-51 EVQLVQSGAEVKKPGESLKISCKGS GYSFTSYWIG.. WVRQMPGKGLEWM GIIYP..GDSDTRYSPSFQG QVTISADKSISTAYLQWS SLKASDTAMYYCAR. IGHV5-78 EVQLLQSAAEVKRPGESLRISCKIS GYSFTSYWIH.. WVRQMPGKGKEWM GSIYP..GNSDTRYSPSFQG HVTISADSSSSTAYLQWS SLKASDAAMYYCVR. Human VH6 germline sequence (SEQ ID NO: 129) VH6 FW1 CDR1 FW2 CDR2 FW3 IGHV6-1 QVQLQQSGPGLVKPSQTLSLTCAIS GDSVSSNSAAWN WIRQSPSRGLEWL GRIYY.RSKWYNDYAVSVKS RITINPDTSKNQFSLQLN SVTPEDTAVYYCAR. Human VH7 germline sequence (from top to bottom, SEQ ID NOs. 130-132): VH7 FW1 CDR1 FW2 CDR2 FW3 IGHV7-4-1 QVQLVQSGSELKKPGASVKVSCKAS GYTFTSYAMN.. WVRQAPGQGLEWM GWINT..NTGNPTYAQGFTG RFVFSLDTSVSTAYLQIC SLKAEDTAVYYCAR. IGHV7-34-1 -LQLVQSGPEVKKPGASVKVSYKSS GYTFIIYGMN.. WV**IPGQGFEWM *WIIT..YTGNPTYTHGFTG WFVFSMDTSVSTACLQIS SLKAEDTAEYYCAR. IGHV7-81 QVQLVQSGHEVKQPGASVKVSCKAS GYSFTTYGMN.. WVPQAPGQGLEWM GWFNT..YTGNPTYAQGFTG RFVFSMDTSASTAYLQIS SLKAEDMAMYYCAR.

TABLE 3 Exemplary Human Vκ germline sequences Human VK1 germline sequence (from top to bottom, SEQ ID NOs. 133-145): VK1 FW1 CDR1 FW2 CDR2 FW3 CDR3 IGKV1-5 DIQMTQSPSTLSASVGDRVTITC RASQ......SISSWLA WYQQKPGKAPKLLIY DASSLES GVPSRFSGSGSGTEF QQYNSYS TLTISSLQPDDFATYYC IGKV1-6 AIQMTQSPSSLSASVGDRVTITC RASQ......GIRNDLG WYQQKPGKAPKLLIY AASSLQS GVPSRFSGSGSGTDF LQDYNYP TLTISSLQPEDFATYYC IGKV1-8 AIRMTQSPSSFSASTGDRVTITC RASQ......GISSYLA WYQQKPGKAPKLLIY AASTLQS GVPSRFSGSGSGTDF QQYYSYP ILTISCLQSEDFATYYC IGKV1-9 DIQLTQSPSFLSASVGDRVTITC RASQ......GISSYLA WYQQKPGKAPKLLIY AASTLQS GVPSRFSGSGSGTEF QQLNSYP TLTISSLQPEDFATYYC IGKV1-12 DIQMTQSPSSVSASVGDRVTITC RASQ......GISSWLA WYQQKPGKAPKLLIY AASSLQS GVPSRFSGSGSGTD QQANSFP FTLTISSLQPEDFATYYC IGKV1-13 AIQLIQSPSSLSASVGDRVTITC RASQ......GISSALA *YQQKPGKAPKLLIY DASSLES GVPSRFSGSGSGTDF QQFNNYP ILTISSLQPEDFATYYC IGKV1-16 DIQMTQSPSSLSASVGDRVTITC RASQ......GISNYLA WFQQKPGKAPKSLIY AASSLQS GVPSRFSGSGSGTDF QQYNSYP TLTISSLQPEDFATYYC IGKV1-17 DIQMTQSPSSLSASVGDRVTITC RASQ......GIRNDLG WYQQKPGKAPKRLIY AASSLQS GVPSRFSGSGSGTEF LQHNSYP TLTISSLQPEDFATYYC IGKV1-27 DIQMTQSPSSLSASVGDRVTITC RASQ......GISNYLA WYQQKPGKVPKLLIY AASTLQS GVPSRFSGSGSGTDF QKYNSAP TLTISSLQPEDVATYYC IGKV1-33 DIQMTQSPSSLSASVGDRVTITC QASQ......DISNYLN WYQQKPGKAPKLLIY DASNLET GVPSRFSGSGSGTDF QQYDNLP TFTISSLQPEDIATYYC IGKV1-37 DIQLTQSPSSLSASVGDRVTITC RVSQ......GISSYLN WYRQKPGKVPKLLIY SASNLQS GVPSRFSGSGSGTDF QRTYNAP TLTISSLQPEDVATYYG IGKV1-39 DIQMTQSPSSLSASVGDRVTITC RASQ......SISSYLN WYQQKPGKAPKLLIY AASSLQS GVPSRFSGSGSGTDF QQSYSTP TLTISSLQPEDFATYYC IGKV1-NL1 DIQMTQSPSSLSASVGDRVTITC RASQ......GISNSLA WYQQKPGKAPKLLLY AASRLES GVPSRFSGSGSGTD QQYYSTP YTLTISSLQPEDFATYYC Human VK1D germline sequence (from top to bottom, SEQ ID NOs. 146-155): VK1D FW1 CDR1 FW2 CDR2 FW3 CDR3 IGKV1D-8 VIWMTQSPSLLSASTGDRVTISC RMSQ......GISSYLA WYQQKPGKAPELLIY AASTLQS GVPSRFSGSGSGTD QQYYSFP FTLTISCLQSEDFATYYC IGKV1D-12 DIQMTQSPSSVSASVGDRVTITC RASQ......GISSWLA WYQQKPGKAPKLLIY AASSLQS GVPSRFSGSGSGTD QQANSFP FTLTISSLQPEDFATYYC IGKV1D-13 AIQLTQSPSSLSASVGDRVTITC RASQ......GISSALA WYQQKPGKAPKLLIY DASSLES GVPSRFSGSGSGTD QQFNNYP FTLTISSLQPEDFATYYC IGKV1D-16 DIQMTQSPSSLSASVGDRVTITC RASQ......GISSWLA WYQQKPEKAPKSLIY AASSLQS GVPSRFSGSGSGTD QQYNSYP FTLTISSLQPEDFATYYC IGKV1D-17 NIQMTQSPSAMSASVGDRVTITC RARQ......GISNYLA WFQQKPGKVPKHLIY AASSLQS GVPSRFSGSGSGTE LQHNSYP FTLTISSLQPEDFATYYC IGKV1D-33 DIQMTQSPSSLSASVGDRVTITC QASQ......DISNYLN WYQQKPGKAPKLLIY DASNLET GVPSRFSGSGSGTD QQYDNLP FTFTISSLQPEDIATYYC IGKV1D-37 DIQLTQSPSSLSASVGDRVTITC RVSQ......GISSYLN WYRQKPGKVPKLLIY SASNLQS GVPSRFSGSGSGTD QRTYNAP FTLTISSLQPEDVATYYG IGKV1D-39 DIQMTQSPSSLSASVGDRVTITC RASQ......SISSYLN WYQQKPGKAPKLLIY AASSLQS GVPSRFSGSGSGTD QQSYSTP FTLTISSLQPEDFATYYC IGKV1D-42 DIQMIQSPSFLSASVGDRVSIIC WASE......GISSNLA WYLQKPGKSPKLFLY DAKDLHP GVSSRFSGRGSGTDF KQDFSYP TLTIISSLKPEDFAAYYC IGKV1D-43 AIRMTQSPFSLSASVGDRVTITC WASQ......GISSYLA WYQQKPAKAPKLFIY YASSLQS GVPSRFSGSGSGTD QQYYSTP YTLTISSLQPEDFATYYC Human VK2 germline sequence (from top to bottom, SEQ ID NOs. 156-162): VK2 FW1 CDR1 FW2 CDR2 FW3 CDR3 IGKV2-4 DIVMTQHLLSLPIPLGEPASISC RSSQSLLHS.DGNTYLD WYLQKPGQSPQLLIY TISNKFY GVPNKFSGSRSGTGF EQGLQGP TLKFSKVEAEDVGVYCC IGKV2-18 DIVMTQTPPSLPVNPGEPASISC RSSQSLLHS.NGYTYLH WYLQKPGQSPQLLIY RVSNHLS GVPDRFSGSGSGSDF MQATQFP TLKISWVEAEDVGVYYC IGKV2-24 DIVMTQTPLSSPVTLGQPASISC RSSQSLVHS.DGNTYLS WLQQRPGQPPRLLIV KISNRFS GVPDRFSGSGAGTDF MQATQFP TLKISRVEAEDVGVYYC IGKV2-28 DIVMTQSPLSLPVTPGEPASISC RSSQSLLHS.NGYNYLD WYLQKPGQSPQLLIY LGSNRAS GVPDRFSGSGSGTDF MQALQTP TLKISRVEAEDVGVYYC IGKV2-29 DIVMTQSPLSLSVTPGQPASISC RSSQSLLHS.DGKTYLY WYLQKPGQSPQLLIY EVSSRFS GVPDRFSGSGSGTDF MQGIHLP TLKISRVEAEDVGVYY* IGKV2-30 DVVMTQSPLSLPVTLGQPASISC RSSQSLVYS.DGNTYLN WFQQRPGQSPRRLIY KVSNRDS GVPDRFSGSGSGTD MQGTHWP FTLKISRVEAEDVGVYYC IGKV2-40 DIVMTQTPLSLPVTPGEPASISC RSSQSLLDSDDGNTYLD WYLQKPGQSPQLLIY TLSYRAS GVPDRFSGSGSGTDF MQRIEEP TLKISRVEAEDVGVYYC Human VK2D germline sequence (from top to bottom, SEQ ID NOs. 163-169): VK2D FW1 CDR1 FW2 CDR2 FW3 CDR3 IGKV2D-18 DIVMTQTPPSLPVNPGEPASISC RSSQSLLHS.NGYTYLH WYPQKPGQSPQLLIY RVSSRFS GVPDRFSGSGSGSDF MQATQFP TLKISWVEAEDVGVYYC IGKV2D-24 DIVMTQTPLSSPVTLGQPASISF RSSQSLVHS.DGNTYLS WLQQRPGQPPRLLIY KVSNRFS GVPDRFSGSGAGTDFT TQATQFP LKISRVEAEDVGVYYC IGKV2D-26 EIVMTQTPLSLSITPGEQASISC RSSQSLLHS.DGYTYLY WFLQKARPVSTLLIY EVSNRFS GVPDRFSGSGSGTDFTL MQDAQDP KISRVEAEDFGVYYC IGKV2D-28 DIVMTQSPLSLSVTPGEPASISC RSSQSLLHS.NGYNYLD WYLQKPGQSPQLLIY LGSNRAS GVPDRFSGSGSGTD MQALQTP FTLKISRVEAEDVGVYYC IGKV2D-29 DIVMTQSPLSLSVTPGQPASISC KSSQSLLHS.DGKTYLY WYLQKPGQPPQLLIY EVSNRFS GVPDRFSGSGSGTD MQSIQLP FTLKISRVEAEDVGVYYC IGKV2D-30 DVVMTQSPLSLPVTLGQPASISC RSSQSLVYS.DGNTYLN WFQQRPGQSPRRLIY KVSNWDS GVPDRFSGSGSGTD MQGTHWP FTLKISRVEAEDVGVYYC IGKV2D-40 DIVMTQTPLSLPVTPGEPASISC RSSQSLLDSDDGNTYLD WYLQKPGQSPQLLIY TLSYRAS GVPDRFSGSGSGTDF MQRIEEP TLKISRVEAEDVGVYYC Human VK3 germline sequence (from top to bottom, SEQ ID NOs. 170-178): VK3 FW1 CDR1 FW2 CDR2 FW3 CDR3 IGKV3-7 EIVMTQSPPTLSLSPGERVTLSC RASQS.....VSSSYLT WYQQKPGQAPRLLIY GASTRAT SIPARFSGSGSGTDF QQDHNLP TLTISSLQPEDFAVYYC IGKV3-11 EIVLTQSPATLSLSPGERATLSC RASQ......SVSSYLA WYQQKPGQAPRLLIY DASNRAT GIPARFSGSGSGTDF QQRSNWP TLTISSLEPEDFAVYYC IGKV3-15 EIVMTQSPATLSLSPGERATLSC RASQ......SVSSNLA WYQQKPGQAPRLLIY GASTRAT GIPARFSGSGSGTEF QQYNNWP TLTISSLQSEDFAVYYC IGKV3-20 EIVLTQSPATLSLSPGERATLSC RASQ......VSSSYLA WYQQKPGQAPRLLIY GASSRAT GIPDRFSGSGSGTDF QQYGSSP TLTISRLEPEDFAVYYC IGKV3-NL1 EIVLTQSPATLSLSPGERATLSC RASQ......SVSSYLA WYQQKPGQAPRLLIY GASTRAT GIPARFSGSGSGTEF Q...... TLTISSLQSEDFAVYYC IGKV3-NL2 EIVLTQSPATLSLSPGERATLSC RASQ......GVSSYLA WYQQKPGQAPRLLIY DASSRAT GIPARFSGSGSGTDF Q...... TLTISSLEPEDFAVYYC IGKV3-NL3 EIVLTQSPGTLSLSPGERATLSC RASQS.....VSSSYLA WYQQKPGLAPRLLIY GASTRAT GIPARFSGSGSGTEF Q...... TLTISRLESEDFAVYYC IGKV3-NL4 EIVLTQSPATLSLSPGERATLSC RASQ......GVSSNLA WYQQKPGQAPRLLIY DASNRAT GIPARFSGSGSGTDF QQRSNWH TLTISSLEPEDFAVYYC IGKV3-NL5 EIVLTQSPATLSLSPGERATLSC RASQS.....VSSSYLA WYQQKPGQAPRLLIY DASSRAT GIPDRFSGSGSGTDF QQRSNWH TLTISRLEPEDFAVYYC Human VK3D germline sequence (from top to bottom, SEQ ID NOs. 179-182): VK3D FW1 CDR1 FW2 CDR2 FW3 CDR3 IGKV3D-7 EIVMTQSPATLSLSPGERATLSC RASQS.....VSSSYLS WYQQKPGQAPRLLIY GASTRAT GIPARFSGSGSGTDF QQDYNLP TLTISSLQPEDFAVYYC IGKV3D-11 EIVLTQSPATLSLSPGERATLSC RASQ.....GVSSYLA WYQQKPGQAPRLLIY DASNRAT GIPARFSGSGPGTDF QQRSNWH TLTISSLEPEDFAVYYC IGKV3D-15 EIVMTQSPATLSVSPGERATLSC RASQ.....SVSSNLA WYQQKPGQAPRLLIY GASTRAT GIPARFSGSGSGTDF QQYNNWP TLTISSLQSEDFAVYYC IGKV3D-20 EIVLTQSPATLSLSPGERATLSC GASQS.....VSSSYLA WYQQKPGLAPRLLIY DASSRAT GIPDRFSGSGSGTDF QQYGSSP TLTISSLEPEDFAVYYC Human VK4 germline sequence (SEQ ID NO: 183) VK4 FW1 CDR1 FW2 CDR2 FW3 CDR3 IGKV4-1 DIVMIQSPDSLAVSLGERATINC KSSQSVLYSSNNKNYLA WYQQKPGQPPKLLIY WASTRES GVPDRFSGSGSGTDF QQYYSTP TLTISSLQAEDVAVYYC Human VK5 germline sequence (SEQ ID NO: 184) VK5 FW1 CDR1 FW2 CDR2 FW3 CDR3 IGKV5-2 ETTLTQSPAFMSATPGDKVNISC KASQ......DIDDDMN WYQQKPGEAAIFIIQ EATTLVP GIPPRFSGSGYGTDF LQHDNFP TLTINNIESEDAAYYFC Human VK6 germline sequence (SEQ ID NO: 185) VK6 FW1 CDR1 FW2 CDR2 FW3 CDR3 IGKV6-21 EIVLIQSPDFQSVTPKEKVTIIC RASQ......SIGSSLH WYQQKPDQSPKLLIK YASQSFS GVPSRFSGSGSGTDF HQSSSLP TLTINSLEAEDAATYYC Human VK6D germline sequence (from top to bottom, SEQ ID NOs. 186-187): VK6D FW1 CDR1 FW2 CDR2 FW3 CDR3 IGKV6D-21 EIVLTQSPDFQSVTPKEKVTITC RASQ......SIGSSLH WYQQKPDQSPKLLIK YASQSFS GVPSRFSGSGSGTDF HQSSSLP TLTINSLEAEDAATYYC IGKV6D-41 DVVMIQSPAFLSVTPGEKVTITC QASE......GIGNYLY WYQQKPDQAPKLLIK YASQSIS GVPSRFSGSGSGTDFTF QQGNKHP TISSLEAEDAATYYC Human VK7 germline sequence (SEQ ID NO: 188) VK7 FW1 CDR1 FW2 CDR2 FW3 CDR3 IGKV7-3 DIVLTQSPASLAVSPGQRATITC RASESVSF..LGINLIH WYQQKPGQPPKLLIY QASNKDT GVPARFSGSGSGTDF LQSKNFP TLTINPVEANDTANYYC

TABLE 4 Exemplary Human V_(λ) germline sequences Human Vλ1 germline sequences (from top to bottom, SEQ ID NOs. 189-196): Vλ1 FW1 CDR1 FW2 CDR2 FW3 CDR3 IGLV1-36 QSVLTQPPSVS SGSSSN..IGNNAVN WYQQLPGKAPKLLIY YDDLL.....PS GVSDRFSGSK..SGTSAS AAWDDSLNG... EAPRQRVTISC LAISGLQSEDEADYYC IGLV1-40 QSVLTQPPSVS TGSSSNI.GAGYDVH WYQQLPGTAPKLLIY GNSNR.....PS GVPDRFSGSK..SGTSAS QSYDSSLSG... GAPGQRVTISC LAITGLQAEDEADYYC IGLV1-41 QSVLTQPPSVS SGSSSD..MGNYAVS WYQQLPGTAPKLLIY ENNKR.....PS GIPDRFSGSK..SGTSAT LAWDTSPRA... AAPGQKVTISC LGITGLWPEDEADYYC IGLV1-44 QSVLTQPPSAS SGSSSN..IGSNTVN WYQQLPGTAPKLLIY SNNQR.....PS GVPDRFSGSK..SGTSAS AAWDDSLNG... GTPGQRVTISC LAISGLQSEDEADYYC IGLV1-47 QSVLTQPPSAS SGSSSN..IGSNYVY WYQQLPGTAPKLLIY RNNQR.....PS GVPDRFSGSK..SGTSAS AAWDDSLSG... GTPGQRVTISC LAISGLRSEDEADYYC IGLV1-50 QSVLTQPPSVS TGSSSNI.GAGYVVH WYQQLPGTAPKLLIY GNSNR.....PS GVPDQFSGSK..SGTSAS KAWDNSLNA... GAPGQRVTISC LAITGLQSEDEADYYC IGLV1-51 QSVLTQPPSVS SGSSSN..IGNNYVS WYQQLPGTAPKLLIY DNNKR.....PS GIPDRFSGSK..SGTSAT GTWDSSLSA... AAPGQKVTISC LGTTGLQTGDEADYYC IGLV1-52 QSVLTQPPSVS TGSSSNTGTGYNVNC WQ*LPRTDPKLLPH GDKNW.....PS WVSDQFSGSK..SGSLAS QSRDIC*VL... WATRQRLTVSC LGTTGIWAEDKTDYHC Human Vλ2 germline sequences (from top to bottom, SEQ ID NOs. 197-205): Vλ2 FW1 CDR1 FW2 CDR2 FW3 CDR3 IGLV2-5 QSALTQPPSVS TGTSSDV.GSYDYVS WYQQHPGTVPKPMIY NVNTQ.....PS GVPDRFSGSK..SGNTAS CSYTSSAT*... GSPGQSVTISC MTISGLQAEDEADY*C IGLV2-8 QSALTQPPSAS TGTSSDV.GGYNYVS WYQQHPGKAPKLMIY EVSKR.....PS GVPDRFSGSK..SGNTAS SSYAGSNNF... GSPGQSVTISC LTVSGLQAEDEADYYC IGLV2-11 QSALTQPRSVS TGTSSDV.GGYNYVS WYQQHPGKAPKLMIY DVSKR.....PS GVPDRFSGSK..SGNTAS CSYAGSYTF... GSPGQSVTISC LTISGLQAEDEADYYC IGLV2-14 QSALTQPASVS TGTSSDV.GGYNYVS WYQQHPGKAPKLMIY EVSNR.....PS GVSNRFSGSK..SGNTAS SSYTSSSTL... GSPGQSITISC LTISGLQAEDEADYYC IGLV2-18 QSALTQPPSVS TGTSSDV.GSYNRVS WYQQPPGTAPKLMIY EVSNR.....PS GVPDRFSGSK..SGNTAS SLYTSSSTF... GSPGQSVTISC LTISGLQAEDEADYYC IGLV2-23 QSALTQPASVS TGTSSDV.GSYNLVS WYQQHPGKAPKLMIY EGSKR.....PS GVSNRFSGSK..SGNTAS CSYAGSSTL... GSPGQSITISC LTISGLQAEDEADYYC IGLV2-33 QSALTQPPFVS TGTSSDV.GDYDHVF WYQKRLSTTSRLLIY NVNTR.....PS GISDLFSGSK..SGIMAS SLYSSSYTF... GAPGQSVTISC LTISGLKSEVEANYHC IGLV2-34 QSVLTQPRSVS TGTSSDI.GGYDLVS WOQ*HPGKAPKLMIY DVANW.....PS GAPGCFSGSK..SGNTAS SSYAGSYNF... RSPGQ*VTIFC LTISGLQAEDEADYYC IGLV2-NL1 QSVLTQPRSVS TGTSSDI.GGYDLVS WOQ*HPGKAPKLMIY DVGNW.....PS GAPGCFSGSK..SGNTAS SSYAGSYNF... RSPGQ*VTIFC LTISGLQAEDEADYYC Human Vλ3 germline sequences (from top to bottom, SEQ ID NOs. 206-218): Vλ3 FW1 CDR1 FW2 CDR2 FW3 CDR3 IGLV3-1 SYELTQPPSVS SGDK....LGDKYAC WYQQKPGQSPVLVTY QDSKR.....PS GIPERFSGSN..SGNTAT QAWDSSTA.... VSPGQTASITC LTISGTQAMDEADYYC IGLV3-9 SYELTQPLSVS GGNN....IGSKNVH WYQQKPGQAPVLVTY PDSNR.....PS GIPERFSGSN..SGNTAT QVWDSSTA.... VALGQTARITC LTISRAQAGDEADYYC IGLV3-10 SYELTQPPSVS SGDA....LPKKYAY WYQQKSGQAPVLVTY EDSKR.....PS GIPERFSGSS..SGTMAT YSTDSSGNH... VSPGQTARITC LTISGAQVEDEADYYC IGLV3-12 SYELTQPHSVS GGNN....IGSYAVH WYQQKPGQDPVLVTY SDSNR.....PS GIPERFSGSN..PGNTTT QVWDSSSDH... VATAQMARITC LTISRTEAGDEADYYC IGLV3-13 SYELTQPPAVS SGDV....LRDNYAD WYPQKPGQAPVLVTY KDGER.....PS GIPERFSGST..SGNTTA FSGD*NN..... VSPGQTARISC LTISRVLTKGGADYYC IGLV3-15 SYELTQPPSVS SGEA....LPKKYAY WYQQKPGQFPVLVTY KDSER.....PS GIPERFSGSS..SGTIVT LSADSSGTY... VSLGQMARITC LTISGVQAEDEADYYC IGLV3-19 SSELTQDPAVS QGDS....LRSYYAS WYQQKPGQAPVLVTY GKNNR.....PS GIPDRFSGSS..SGNTAS NPRDSSGNH... VALGQTVRITC LTITGAQAEDEADYYC IGLV3-21 SYVLTQPPSVS GGNN....IGSKSVH WYQQKPGQAPVLVTY YDSDR.....PS GIPERFSGSN..SGNTAT QVWDSSSDH... VAPGKTARITC LTISRVEAGDEADYYC IGLV3-22 SYELTQLPSVS SGDV....LGENYAD WYQQKPGQAPELVTY EDSER.....YP GIPERFSGST..SGNTTT LSGDEDN..... VSPGQTARITC LTISRVLTEDEADYYC IGLV3-25 SYELNQPPSVS SGDA....LPKQYAY WYQQKPGQAPVLVTY KDSER.....PS GIPERFSGSS..SGTTVT QSADSSGTY... VSPGQTARITC LTISGVQAEDEADYYC IGLV3-27 SYELTQPSSVS SGDV....LAKEYAR WFQQKPGQAPVLVTY KDSER.....PS GIPERFSGSS..SGTTVT YSAADNN..... VSPGQTARITC LTISGAQVEDEADYYC IGLV3-31 SSELSQEPAVS QGDS....IEDSVVN WYKQKPSQAPGLVT* INSVQ.....SS GIPKKFSGSS..SGNMAT QSWDSSRTH... VALG*TARITC LTITGTQVEDKADYYC IGLV3-32 SSGPTQVPAVS QGDS....MEGSYEH WYQQKPGQAPVLVTY DSSDR.....PS GIPERFSGSE..SGNTTT QLIDNHA..... VALGQMARITC LTITGAQAEDEADYYT Human Vλ4 germline sequences (from top to bottom, SEQ ID NOs. 219-221): Vλ4 FW1 CDR1 FW2 CDR2 FW3 CDR3 IGLV4-3 LPVLTQPPSAS TLSSE...HSTYTIE WYQQRPGRSPQYIMK VKSDGSHSK.GD GIPDRFMGSS..SGADRY GESHTTDGQVG* ALLGASIKLTC LTFSNLQSDDEAEYHC IGLV4-50 QPVLTQSSSAS TLSSG...HSSYIIA WHQQQPGKAPRYLMK LEGSGSYNK.GS GVPDRFSGSS..SGADRY ETWDSNT..... ASLGSSVKLTC LTISNLQLEDEADYYC IGLV4-59 QPVLTQSPSAS TLSSG...HSSYAIA WHQQQPEKGPRYLMK LNSDGSHSK.GS GIPDRFSGSS..SGAERY QTWGTGI..... ASLGASVKLTC LTISSLQSEDEADYYC Human Vλ5 germline sequences (from top to bottom, SEQ ID NOs. 222-2261): Vλ5 FW1 CDR1 FW2 CDR2 FW3 CDR3 IGLV5-37 QPVLTQPPSSSA TLPSDIN.VGSYNIY WYQQKPGSPPRYLLY YYSDSDKGQ.GS GVPSRFSGSKDASANTGI MIWPSNAS.... SPGESARLTC LLISGLQSEDERDYYC IGLV5-39 QPVLTQPTSLSA TLRSDIN.VGTYRIY WYQQKPGSLPRYLLR YKSDSDKQQ.GS GVPSRFSGSKDASTNAG AIWYSSTS.... SPGASARFTC LLLISGLQSEDEADYYC IGLV5-45 QAVLTQPASLSA TLRSGIN.VGTYRIY WYQQKPGSPPQYLLR YKSDSDKQQ.GS GVPSRFSGSKDASANAGI MIWHSSAS.... SPGASASLTC LLISGLQSEDEADYYC IGLV5-48 QPVLTQPTSLSA TLRSGIN.LGSYRIF WYQQKPESPPRYLLS YYSDSSKRQ.GS GVPSRFSGSKDASSNAGI MIWHSSAS.... SPGASARLTC LVISGLQSEDEADYYC IGLV5-52 QPVLTQPSSHSA MLSSGFS.VGDFWIR WYQQKPGNPPRYLLY YHSDSNKGQ.GS GVPSRFSGSNDASANAGI GTWHSNSKT... SSGASVRLTC LRISGLQPEDEADYYC Human Vλ6 germline sequences (SEQ ID NOs. 227) Vλ6 FW1 CDR1 FW2 CDR2 FW3 CDR3 IGLV6-57 NFMLTQPHSVSE TPSSGS..IASNYVQ WYQQROGSSOTTVIY EDNQR.....PS GVPDRFSGSIDSSSNSAS QSYESSN..... SPGKTVTISC LTISGLKTEDEADYYC Human Vλ7 germline sequence (from top to bottom, SEQ ID NOs. 228-229): Vλ7 FW1 CDR1 FW2 CDR2 FW3 CDR3 IGLV7-43 QTVVTQEPSLTV ASSTGAV.TSGYYPN WFQQKPGQAPRALIY STSNK.....HS WTPARFSGSL..LGGKAA LLYYGGAQ.... SPGGTVTLTC LTLSGVQPEDEAEYYC IGLV7-45 QAVVTQEPSLTV GSSTGAV.TSGHYPY WFQQKPGQAPRTLIY DTSNK.....HS WTPARFSGSL..LGGKAA LLSYSGAR.... SPGGTVTLTC LTLSGAQPEDEAEYYC Human Vλ8 germline sequence (SEQ ID NO: 230) VλD FW1 CDR1 FW2 CDR2 FW3 CDR3 IGLV8-61 QTVVTQEPSFSV GLSSGSV.STSYYPS WFQQTPGQAPRTLIY STNTR.....SS GVPDRFSGSI..LGNKAA VLYMGSGI.... SPGGTVTLTC LTITGAQADDESDYYC Human Vλ9 germline sequence (SEQ ID NO: 231) Vλ9 FW1 CDR1 FW2 CDR2 FW3 CDR3 IGLV9-49 QPVLTQPPSASA TLSSG...YSNYKVD WQQQRPGKGPRFMVR VGTGGIVGSKGD GIPDRFSVLG..SGLNRY GADHGSGSNFV* SLGASVTLTC LTIKNIQEEDESDYHC Human Vλ10 germline sequence (SEQ ID NO: 232) Vλ10 FW1 CDR1 FW2 CDR2 FW3 CDR3 IGLV10-54 QAGLTQPPSVSK TGNSNN..VGNQGAA WLQQHQGHPPKLLSY RNNNR.....PS GISERLSASR..SGNTAS SAWDSSLSA... GLRQTATLTC LTITGLQPEDEADYYC Human Vλ11 germline sequence (SEQ ID NO: 233) Vλ11 FW1 CDR1 FW2 CDR2 FW3 CDR3 IGLV11-55 RPVLTQPPSLSA TLSSDLS.VGGKNMF WYQQKPGSSPRLFLY HYSDSDKQL.GP GVPSRVSGSKETSSNTAF QVYESSAN.... SPGATARLPC LLISGLQPEDEADYYC

TABLE 5 Exemplary Human Germline Heavy Chain Consensus Sequence Consensus VH FW1 CDR1 FW2 CDR2 FW3 CDR3 All-VH EVQLVESGGGLVKP GFTFSSYAMX-- WVRQAPGKGLEWV GWISP--NGGSTYYADSVKG RFTISRDNSKNTLYLQMN GGSLRLSCAAS SLRAEDTAVYYCAR- All-VH+ EVQLVESGGGLVKP GFTFSSYAMXWS WVRQAPGKGLEWV GWISPKANGGSTYYADSVKG RFTISRDNSKNTLYLQMN GGSLRLSCAAS SLRAEDTAVYYCARX VH1 QVQLVQSGAEVKKP GYTFTSYXXM-- WVRQAPGQGLEWV GWINP--XNGNTNYAQKEQG RVTITRDTSTSTAYMELS GASVKVSCKAS SLRSEDTAVYYCAR- VH2 QVTLKESGPALVKP GFSLSTSGMGVX WIRQPPGKALEAL AXIY---WNDDKYYSXSLES RLTISKDTSKNQVVLTMT TQTLTLTCTFS NMDPVDTATYYCARX VH3 EVQLVESGGGLVQP GFTFSSYAMS-- WVRQAPGQGLEWV SVISS--DGXSTYYADSVKG RFTISRDNSKNSLYLQMN GGSLRLSCAAS SLRAEDTAVYYCARX VH3+ EVQLVESGGGLVQP GFTFSSYAMS-- WVRQAPGKGLEWV SVISSKADGXSTYYADSVKG RFTISRDNSKNSLYLQMN GGSLRLSCAAS SLRAEDTAVYYCARX VH4 QVQLQESGPGLVKP GGSISSGXYYS- WIRQPPGKGLEWI GYIY--YSGSTYYNPSLKS RVTISVDTSKNQESLKLS SETLSLTCAVS SVTAADTAVYYCAR- VH4+ QVQLQESGPGLVKP GGSISSGXYYWS WIRQPPGKGLEWI GYIY--YSGSTYYNPSLKS RVTISVDTSKNQESLKLS SETLSLTCVAS SVTAADTAVYYCAR- VH5 EVQLVQSGAEVKKP GYSFTSYWIX-- WVRQMPGKGLEWS GXIYP--GDSDTRYSPSEQG HVTISADKSISTAYLQNS GESLRISCKGS SLKASDTAMYYCAR- VH6 QVQLQQSGPGLVKP GDSVSSNSAAWN WIRQSPSRGLEWL GRTYYR-SKWYNDYAVSVKS RITINPDTSKNQESLQIN SQTLSLTCAIS SVTPEDTAVYYCAR- VH7 QVQLVQSGXEXRXP GYXFTXYXMN-- WVXQAPGQGLEWS GWXNT--XTGNPTYAQGETG REVESXDTSXSTAYLQIX GASVKVSCKAS SLKAEDXAXYYCAR- +Consensus sequence where consensus gaps are replaced with most common amino acid From top to bottom: SEQ ID NOs. 234-244.

TABLE 6 Exemplary Human Germline Light Chain Consensus Sequence Vλ germline consensus sequences Consensus Vλ FW1 CDR1 FW2 CDR2 FW3 CDR3 All-VL QSVLTQPPSV TGSSS--GGSYYVS WYQQKPGQAPKLLIY EDSNR-----PS GVPDRFSGSK--SGNTAS QSWDSSAXF--- SVSPGQSVTITC LTISGLQAEDEADYYC All-VL+ QSVLTQPPSV TGSSSDVGGSYYVS WYQQKPGQAPKLLIY EDSNRXRXQKPS GVPDRFSGSKDASGNTAS QSWDSSAXFXXX SVSPGQSVTITC LTISGLQAEDEADYYC VL1 QSVLTQPPSV SGSSSN-INGNNXVX WYQQLPGTAPKLLIY GNNXR-----PS GVPDRFSGSK--SGTSAS AAWDDSLXG--- SGAPGQRVTISC LAIIGLQSEDEADYYC VL1+ QSVLTQPPSV SGSSSNIIGNNXVX WYQQLPGTAPKLLIY GNNXR-----PS GVPDRFSGSK--SGTSAS AAWDDSLXG--- SGAPGQRVTISC LAIIGLQSEDEADYYC VL2 QSALTQPPSV TGTSSDVGGYNYVS WYQQHPGKAPKIMIY EVSNR-----PS GVPDRFSGSK--SGNTAS SSYAGSYTF--- SGSPGQSVTISC LTISGLQAEDEADYYC VL3 SYELTQPPSV SGDX---LGXKYAH WYQQKPGQAPVLVIY KDSER-----PS GIPERFSGSS--SGNTAT QSWDSSG----- SVSPGQTARITC LTISGXQAEDEADYYC VL3+ SYELTQPPSV SGDX---LGXKYAH WYQQKPGQAPVLVIY KDSER-----PS GIPERFSGSS--SGNTAT QSWDSSGXH--- SVSPGQTARITC LTISGXQAEDEADYYC VL4 QPVLTQSPSA TLSSG--HSSYXIA WHQQQPGKXPRYLMK LXSDGSHSK-GD GIPDRFSGSS--SGADRY XIWXTXX----- SASLGASVRLTC LTISNLQSEDEADYYC VL4+ QPVLTQSPSA TLSSG--HSSYXIA WHQQQPGKXPRYLMK LXSDGSHSK-GD GIPDRFSGSS--SGADRY XIWXTXXGQVG- SASLGASVRLTC LTISNLQSEDEADYYC VL5 QPVLTQPTSL TLRSGINVGXYRIY WYQQKPGSPPRYLLX YXSDSDKXQ-GS GVPSRFSGSKDASANAGI MIWHSSAS---- SASPGASARLTC LLISGLQSEDEADYYC VL5+ QPVLTQPTSL TLRSGINVGXYRIY WYQQKPGSPPRYLLX YXSDSDKXQ-GS GVPSRFSGSKDASANAGI MIWHSSASI--- SASPGASARLTC LLISGLQSEDEADYYC VL6 NFMLTQPKSV TRSSGS-IASNYVQ WYQQRPGSSPTTVIY EDNQR-----PS GVPDRFSGSIDSSSNSAS QSYDSSN----- SESPGRTVTISC LTISGLKTEDEADYYC VL7 QXVVTQEPSL XSSTGAVTSGXYPX WFQQKPGQAPRXLIY NISNK-----HS WIPARFSGSL--LGGKAA LLXYXGAX---- IVSPGGTVTLTC LTISGXQPEDEAEYYC VL8 QTVVTQEPSF GLSSGSVSTSYYPS WYQQTPGQAPRTLIY STNTR-----SS GVPDRFSGSI--LGNKAA VLYXGSGI---- SVSPGGTVTLTC LTITGAQADDESDYYC VL9 QPVLTQPPSA TLSSG--YSNYRVD WYQQRPGKGPRFVMR VGTGGTVGSRGD GIPDRFSVLG--SGLNRY GADHGSGSNFV- SASLGASVTLTC LTIKNIQEEDESDYHC VL10 QAGLTQPPSV TGNSNN-VGNQAA WLQQHQGHPPKLLSY RNDDNR-----PS GISERLSASR--SGNTAS SAWDSSLSA--- SKGLRQTATLTC LTITGLQPEDEADYYC VL11 RPVLTQPPSL TLSSDLSVGGKNMF WYQQKPGSSPRLFLY HYSDSDKQL-GP GVPSRVSGSKETSSNTAF QVYESSAN---- SASPGATARLPC LLISGLQPEDEADYYC +Consensus sequence where consensus gaps are replaced with most common amino acid From top to bottom: SEQ ID NOs. 245-261. VK germline consensus sequences Consensus VK FW1 CDR1 FW2 CDR2 FW3 CDR3 All-VK DIVMTQSPSS RASQ------GISSYLA WYQQKPGQAPKLLIY AASSRAS GVPSRFSGSGSGTDFTLT QQYNSYP LSASPGERATISC ISSLQPEDFAVYYC All-VK+ DIVMTQSPSS RASQSLLHSDGISSYLA WYQQKPGQAPKLLIY AASSRAS GVPSRFSGSGSGTDFTLT QQYNSYP LSASPGERATISC ISSLQPEDFAVYYC VK1 DIQMTQSPSS RASQ------GISXYLA WYQQKPGKAPKLLIY AASSLQS GVPSRFSGSGSGTDFTLT QQYNSYP LSASVGDRVTITC ISSLQPEDFATYYC VK1D DIQMTQSPSS RASQ------GISSYLA WYQQKPGKAPKLLIY AASSLQS GVPSRFSGSGSGTDFTLT QQYNSYP LSASVGDRVTITC ISSLQPEDFATYYC VK2 DIVMTQTPLS RSSQSLLHSD-GNTYLD WYLQKPGQSPQLLIY XXSNRXS GVPDRFSGSGSGTDFTLK MQATQFP LPVTXGEPASISC ISRVEAEDVGVYYC VK2+ DIVMTQTPLS RSSQSLLHSDDGNTYLD WYLQKPGQSPQLLIY XXSNRXS GVPDRFSGSGSGTDFTLK MQATQFP LPVTXGEPASISC ISRVEAEDVGVYYC VK2D DIVMTQTPLS RSSQSLLHS-DGXTYLX WYLQKPGQSPQLLIY XVSNRFS GVPDRFSGSGSGTDFTLK MQATQFP LPVTPGEPASISC ISRVEAEDVGVYYC VK2D+ DIVMTQTPLS RSSQSLLHSDDGXTYLX WYLQKPGQSPQLLIY XVSNRFS GVPDRFSGSGSGTDFTLK MQATQFP LPVTPGEPASISC ISRVEAEDVGVYYC VK3 EIVLTQSPAT RASQS-----VVSSYLA WYQQKPGQAPRLLIY GASTRAT GIPARFSGSGSGTDFTLT QQRSNWP LSLSPGERATLSC ISSLEPEDFAVYYC VK3D EIVXTQSPAT RASQS-----VXSSYLA AWQQKPGQAPRLLIY XASTRAT GIPARFSGSGSGTDFTLT QQYXNWP LSLSPGERATLSC ISSLXPEDFAVYYC VK4 DIVMTQSPDS RSSQSVLYSSNNKNYLA WYQQKPGQPPKLLIY RASTRES GVPDRFSGSGSGTDFTLT QQYYSTP LAVSLGERATINC ISSLQAEDVAVYYV VK5 XIVLTQSPXF RASX------SIGXSLH WYQQKPDQSPKLLIK YASQSFS GVPSRFSGSGSGTDFTLT HQSSSLP XSVTPXEKVTITC INSLEAEDAATYYC VK5+ XIVLTQSPXF RASXSVSF--SIGXSLH WYQQKPDQSPKLLIK YASQSFS GVPSRFSGSGSGTDFTLT HQSSSLP XSVTPXEKVTITC INSLEAEDAATYYC VK5 EIVLTQSPDF RASQ------SIGSSLH WYQQKPDQSPKLLIK YASQSFS GVPSRFSGSGSGTDFTLT HQSSSLP QSVTPKEKVTITC INSLEAEDAATYYC VK5D XXVXTQSPXF XASX------XIGXXLX WYQQKPDQXPKLLIK YASQSXS GVPSRFSGSGSGTDFTXT XQXXXXP XSVTPXEKVTITC IXSLEAEDAATYYC VK7 DIVLTQSPAS RASESVS--FLGINLIH WYQQKPGQPPKLLIY QASNRDT GVPARFSGSGSGTDFTLT LQSKNFP LAVSPGQRATITC INPVEANDTANYYC +Consensus sequence where consensus gaps are replaced with most common amino acid From top to bottom: SEQ ID NOs. 262-277.

TABLE 7 Sequence alignment of CDR-humanized anti-A33 antibodies A33 Rabbit ELVMTQTPPSLSASVGETVRIRC L AS EFLFNGVS WYQQKPGKPPKFLIS G AS N L E SGVPP RFSGSGSGTDYTLTIGGVQAEDVATYYC LGG YS GSSG LTFGAGTNVEIK DPK9/JK4 DIQMTQSPSSLSASVGDRVTITCRASQSISSYLNWYQQKPGKAPKLLIYAASSLQSGVPS RFSGSGSGTDFTLTISSLQPEDFATYYCQQSYS  TPLTFGGGTKVEIK ABS-A33-1 DIQMTQSPSSLSASVGDRVTITCRASQSISSY VS WYQQKPGKAPKLLIY G AS N LQSGVPS RFSGSGSGTDFTLTISSLQPEDFATYYC LGG YSGST G LTFGGGTKVEIK ABS-A33-2 DIQMTQSPSSLSASVGDRVTITCRAS EFLFNGVS WYQQKPGKAPKLLIY G ASSL E SGVPS RFSGSGSGTDFTLTISSLQPEDFATYYC QGG YSGS SG LTFGGGTKVEIK ABS-A33-3 DIQMTQSPSSLSASVGDRVTITCRAS E SLSSYL S WYQQKPGKAPKLLIY G AS N LQSGVPS RFSGSGSGTDFTLTISSLQPEDFATYYC LGG YSGS SG LTFGGGTKVEIK ABS-A33-4 DIQMTQSPSSLSASVGDRVTITCRAS QFLFN GL S WYQQKPGKAPKLLIY G AS N LQSGVPS RFSGSGSGTDFTLTISSLQPEDFATYYC QGG YSGST G LTFGGGTKVEIK ABS-A33-6 DIQMTQSPSSLSASVGDRVTITCRAS QFLFNGVS WYQQKPGKAPKLLIYAAS N L E SGVPS RFSGSGSGTDFTLTISSLQPEDFATYYC QGG YSGST G LTFGGGTKVEIK ABS-A33-7 DIQMTQSPSSLSASVGDRVTITCRAS EFLFNGVS WYQQKPGKAPKLLIYAASSLQSGVPS RFSGSGSGTDFTLTISSLQPEDFATYYC QGG YSGS SG LTFGGGTKVEIK ABS-A33-8 DIQMTQSPSSLSASVGDRVTITCRAS QFLFNGVS WYQQKPGKAPKLLIYAAS N LQSGVPS RFSGSGSGTDFTLTISSLQPEDFATYYC QGG YSGS SG LTFGGGTKVEIK ABS-A33-9 DIQMTQSPSSLSASVGDRVTITCRAS QFLFN VLVWYQQKPGKAPKLLIYAAS N L E SGVPS RFSGSGSGTDFTLTISSLQPEDFATYYC QGG YSGST G LTFGGGTKVEIK ABS-A33-10 DIQMTQSPSSLSASVGDRVTITCRAS EFLFNGVS WYQQKPGKAPKLLIY G ASSL E SGVPS RFSGSGSGTDFTLTISSLQPEDFATYYC QGG YSGS SG LTFGGGTKVEIK ABS-A33-11 DIQMTQSPSSLSASVGDRVTITCRAS EFLFNGVS WYQQKPGKAPKLLIY G ASSL E SGVPS RFSGSGSGTDFTLTISSLQPEDFATYYC QGG YSGS SG LTFGGGTKVEIK A33 Rabbit QEQLMESGGGLVTLGGSLKLSCKASG ID FS H Y GI SWVRQAPGKGLEWIA Y I YPNY GS VD YA SW V N G RFTISLDNAQNTVFLQMISLTAADTATYFCAR DRGYYSGSRGTRLDL WGQGTLVTISS DP47/JH4 EVQLLESGGGLVQPGGSLRLSCAASGFTFSSYAMSWVRQAPGKGLEWVSAISGSGGSTYYADSVKG RFTISRDNSKNTLYLQMNSLRAEDTAVYYCAK               WGQGTLVTVSS ABS-A33-1 EVQLLESGGGLVQPGGSLRLSCAASGF D FSSYAMSWVRQAPGKGLEWVSAIS PN GGSVYYADSV N G RFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKDRGYYTGSRGTRLALWGQGTLVTVSS ABS-A33-2 EVQLLESGGGLVQPGGSLRLSCAASGFTFS H Y GI SWVRQAPGKGLEWVS Y I YPNY GST D YADSVKG RFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKDRQYYSGSRGTRLDLWGQGTLVTVSS ABS-A33-3 EVQLLESGGGLVQPGGSLRLSCAASGFTFSSYAISWVRQAPGKGLEWVS Y I Y G N GGS VD YA SW V N G RFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKDRVYYSVSRGTRLDLWGQGTLVTVSS ABS-A33-4 EVQLLESGGGLVQPGGSLRLSCAASGF D FS H Y GI SWVRQAPGKGLEWVS Y I YP S Y GST D YADSVKG RFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKDRGYYSGSRGTRLDLWGQGTLVTVSS ABS-A33-6 EVQLLESGGGLVQPGGSLRLSCAASGFTFS H Y GI SWVRQAPGKGLEWVS Y I YP S Y GST D YASSVKG RFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKDRGAYSGSRGTRLDLWGQGTLVTVSS ABS-A33-7 EVQLLESGGGLVQPGGSLRLSCAASG ID FSSY GI SWVRQAPGKGLEWVS Y I YP S Y GST D YAD W VKG RFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKDRGYYSGSRGTRLDLWGQGTLVTVSS ABS-A33-8 EVQLLESGGGLVQPGGSLRLSCAASG ID FSSY GI SWVRQAPGKGLEWVS Y I YP S Y GST D YA SW V N G RFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKDRGVYSGSRGTRLDLWGQGTLVTVSS ABS-A33-9 EVQLLESGGGLVQPGGSLRLSCAASG ID FS H Y GI SWVRQAPGKGLEWVS Y I YPNY GST D YA SW V N G RFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKDKGYYSGSRGTRLDLWGQGTLVTVSS ABS-A33-10 EVQLLESGGGLVQPGGSLRLSCAASGFTFS H YG ISWVRQAPGKGLEWVS Y I YPNY GST D YADSVKG RFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKDRQYYSGSRGTRLDLWGQGTLVTVSS A33 Rabbit = rabbit anti-A33 v-gene sequences. CDRs in bold. From Top to Bottom: SEQ ID NOs. 353-375.

TABLE 8 Sequence alignment of CDR-humanized antib-pTau antibodies pT231 pTau   ALTQPTSVSANLGGSVEITC S G SD -- YD Y G -WYQQKAPGSAPVTVIY WNDK RPSDIPS RFSGSTSGSTSTLTITGVQAEDEAVYYC GAY DGS AGGGI FGAGTTLTVL DPL16/Jλ2 SSELTQDPAVSVALGQTVRITCQGDSLRSYYASWYQQK-PGQAPVLVIYGKNNRPSGIPD RFSGSSSGNTASLTITGAQAEDEADYYCNSRDSSGNHVVFGGGTKLTVL C11-ABS-pTAU SSELTQDPAVSVALGQTVRITCQGD D --SYY G -WYQQK-PGQAPVTVIYG N NNRPSGIPD RFSGSSSGNTASLTITGAQAEDEADYYC GAY DGSG G H G VFGGGTKLTVL C9-ABS-pTAU SSELTQDPAVSVALGQTVRITC S GD D --SYY G -WYQQK-PGQAPVTVIYG N NNRPSGIPD RFSGSSSGNTASLTITGAQAEDEADYYC GAY DGSG G H G VFGGGTKLTVL C18-ABS-pTAU SSELTQDPAVSVALGQTVRITCQGD D --SYY G -WYQQK-PGQAPVTVIYG NDK RPSGIPD RFSGSSSGNTASLTITGAQAEDEADYYC GAY DGSG GGG VFGGGTKLTVL C4-ABS-pTAU SSELTQDPAVSVALGHTVRITC S GD D --SYY G -WYQQK-PGQAPVTVIYG N NNRPSGIPD RFSGSSSGNTASLTITGAQAEDEADYYC GAY DSSG GGGI FGGGTKLTVL C13-ABS-pTAU SSELTQDPAVSVALGQTVRITCQGD D --SYY G -WYQQK-PGQAPVTVIYG N N K RPSGIPD RFSGSSSGNTASLTITGAQAEDEADYYC GAY DSSG GGG VFGGGTKLTVL C21-ABS-pTAU SSELTQDPAVSVALGQTVRITCQGD D --SYY G -WYQQK-PGQAPVTVIYG ND NRPSGIPD RFSGSSSGNTASLTITGAQAEDEADYYC GAY DSSG GGGI FGGGTKLTVL C6-ABS-pTAU SSELTQDPAVSVALGQTVRITCQGD D --SYY G -WYQQK-PGQAPVTVIYG ND NRPSGIPD RFSGSSSGNTASLTITGAQAEDEADYYC GAY DSSG GGGI FGGGTKLTVL C8-ABS-pTAU SSELTQDPAVSVALGQTVRITCQG SD -- Y YY G -WYQQK-PGQAPVTVIYG ND NRPSGIPD RFSGSSSGNTASLTITGAQAEDEADYYC G S Y DSS AG H G VFGGGTKLTVL pT231 pTau AVTLDESGGGLQTPGGGLSLVCKASGFT L SSY Q M M WVRQAPGKGLEWVAGITSRGGVTGYGSAVKG RATISRDNGQSTVRLQLNNLRAEDTGTYYCAK PALDSDQCGFPEAGC ID A WGHGTEVIVSS DP47/JH4 EVQLLESGGGLVQPGGSLRLSCAASGFTFSSYAMSWVRQAPGKGLEWVSAISGSGGSTYYADSVKG RFTISRDNSKNTLYLQMNSLRAEDTAVYYCAK               FDYWGQGTLVTVSS C11-ABS-pTAU EVQLLESGGGLVQPGGSLRLSCKASGFTFSSY Q M M WVRQAPGKGLEWVAGITSRGGVTGYGDSVKG RFTISRDNSKNTLYLQMNSLRAEDTAVYYCAK PALDSDQCGFPEAGCI D A WGQGTLVTVSS C09-ABS-pTAU EVQLLESGGGLVQPGGSLRLSCKASGFTFSSY Q M M WVRQAPGKGLEWVAGITSRGGVTGYADAVKG RFTISRDNSKNTLYLQMNSLRAEDTAVYYCAK PALDADQCGFPEAGCI D A WGQGTLVTVSS C18-ABS-pTAU EVQLLESGGGLVQPGGSLRLSCKASGFTFSSY Q M M WVRQAPGKGLEWVAGITSRGGVTGYGSAVKG RFTISRDNSKNTLYLQMNSLRAEDTAVYYCAK PALDSDQCGFPEAGCI D S WGQGTLVTVSS C04-ABS-pTAU EVQLLESGGGLVQPGGSLRLSCKASGFTFSSY Q MSWVRQAPGKGLEWVAGITSRGGVTGYGDAVKG RFTISRDNSKNTLYLQMNSLRAEDTAVYYCAK PALDADQCGFPEAGCI D A WGQGTLVTVSS C13-ABS-pTAU EVQLLESGGGLVQPGGSLRLSCKASGFTFSSY Q M M WVRQAPGKGLEWVSGITSRGGVTGYADSVKG RFTISRDNSKNTLYLQMNSLRAEDTAVYYCAK PALDSDQCGFPEAGCI D A WGQGTLVTVSS C21-ABS-pTAU EVQLLESGGGLVQPGGSLRLSCKASGFT L SSY Q M M WVRQAPGKGLEWVAGITSRGGVTGYGDSVKG RFTISRDNSKNTLYLQMNSLRAEDTAVYYCAK PALDSDQCGFPEAGCI D A WGQGTLVTVSS C06-ABS-pTAU EVQLLESGGGLVQPGGSLRLSCKASGFTFSSY Q M M WVRQAPGKGLEWVSGITSRGGVTGYGSSVKG RFTISRDNSKNTLYLQMNSLRAEDTAVYYCAK PALNSDQCGFPEAGCI D A WGQGTLVTVSS C08-ABS-pTAU EVQLLESGGGLVQPGGSLRLSCKASGFTFSSY Q MSWVRQAPGKGLEWVSGITGRGGVTGYADAVKG RFTISRDNSKNTLYLQMNSLRAEDTAVYYCAK PALDSDQCGFPEAGCI D A WGQGTLVTVSS From Top to Bottom: SEQ ID NOs. 376-395.

TABLE 9 Sequence alignment of CDR-humanized anti-RAGE antibodies XTM4 RAGE DIQMTQSPSSMSVSLGDTITITCRASQ DVGI Y V NWFQQKPGKSPRRMIY R A TN L AD GVPSRFSGSRSGSIYS LTISSLESEDVADYHC LEFDEH PLTFGSGTKVEIK DPK9/JK4 DIQMTQSPSSLSASVGDRVTITCRASQSISSYLNWYQQKPGKAPKLLIYAASSLQSGYPSRFSGSGSGTDFTL TISSLQPEDFATYYCQQSYSTPLTFGGGTKVEIK C4-ABS-RAGE DIQMTQSPSSLSASVGDRVTITCRASQS VG SY V NWYQQKPGKAPKLLIY R ASSL AD GVPSRFSGSGSGT DFTLTISSLQPEDFATYYC LEFDEH PLTFGGGTKVEIK C11-ABS-RAGE DIQMTQSPSSLSASVGDRVTITCRASQS VG SY V NWYQQKPGKAPKLLIY R AS N LQSGVPSRFSGSGSG TDFTLTISSLQPEDFATYYC LEFDEH PLTFGGGTKVEIK C10-ABS-RAGE DIQMTQSPSSLSASVGDRVTITCRASQ DVG SY V NWYQQKPGKAPKLLIY R AS N L AD GVPSRFSGSGSG TDFTLTISSLQPEDFATYYCQ EF YS H PLTFGGGTKVEIK C3-ABS-RAGE DIQMTQSPSSLSASVGDRVTITCRASQSISSYLNWYQQKPGKAPKLLIY R A TN LQSGVPSRFSGSGSGTDF TLTISSLQPEDFATYYC LEFDEH PLTFGGGTKVEIK C7-ABS-RAGE DIQMTQSPSSLSASVGDRVTITCRASQSI G SYLNWYQQKPGKAPKLLIY R ASSL A SGVPSRFSGSGSGTD FTLTISSLQPEDFATYYC LEFDEH PLTFGGGTKVEIK XTM4 RAGE EVQLVESGGGLVQPGRSLKLSCVVSGFTF NN YWM T WIRQTPGKGLEWVA S I DNS G DNT YY P DSVK D RFTIS RDNAKSTLYLQMNSLRSEDTATYYCTR GGDITTGF DYWGQGVMVTVSS DP54/JH4 EVQLVESGGGLVQPGGSLRLSCAASGFTFSSYWMSWVRQAPGKGLEWVANIKQDGSEKYYVDSVKGRFTISR DNAKNSLYLQMNSLRAEDTAVYYCAR        DYWGQGTLVTVSS C4-ABS-RAGE EVQLVESGGGLVQPGGSLRLSCAASGFTFS N YWMSWVRQAPGKGLEWVA S IKNDGD NTY YVDSVKDRFT ISRDNAKNSLYLQMNSLRAEDTAVYYCAR GGDITTGLD YWGQGTLVTVSS C11-ABS-RAGE EVQLVESGGGLVQPGGSLRLSCAAS GFTFS N YWMSWVRQAPGKGLEWVAT S I DNS GS N KYYVDSVKGRFT ISRDNAKNSLYLQMNSLRAEDTAVYYCAR GGDITTGF DYWGQGTLVTVSS C10-ABS-RAGE EVQLVESGGGLVQPGGSLRLSCAASGFTFSSYWMSWVRQAPGKGLEWVA S IK NS GSE T YY P DSVKGRFT ISRDNAKNSLYLQMNSLRAEDTAVYYCAR GGDITTGF DYWGQGTLVTVSS C3-ABS-RAGE EVQLVESGGGLVQPGGSLRLSCAASGFTFSSYWMSWVRQAPGKGLEWVA S I D QDGSEKYY P DSVKGRFT ISRDNAKNSLYLQMNSLRAEDTAVYYCAR GGDITTGL DYWGQGTLVTVSS C7-ABS-RAGE EVQLVESGGGLVQPGGSLRLSCAASGFTFSSYWMSWVRQAPGKGLEWVA S I D QDGS N KYY P DSVKGRFT ISRDNAKNSLYLQMNSLRAEDTAVYYCAR GGDITTGL DYWGQGTLVTVSS XTM4 RAGE = rat anti-RAGE v-gene sequences. From Top to Bottom: SEQ ID NOs. 396-409. 

What is claimed is:
 1. An isolated humanized monoclonal antibody or antigen-binding fragment thereof that binds to a target antigen prepared by a method comprising, (1) obtaining the sequence of a non-human donor antibody that binds to said target antigen, and determining the donor CDR-L1, CDR-L2, CDR-L3, CDR-H1, and CDR-H2 sequences of said non-human donor antibody; (2) obtaining the sequences of a human germline VL and a human germline VH, and determining the germline framework and germline CDR-L1, CDR-L2, CDR-L3, CDR-H1, and CDR-H2 sequences of said human VL and VH; (3) aligning each of the non-human donor CDR-L1, CDR-L2, and CDR-L3 sequences with the corresponding germline CDR sequence from said human VL, and each of the non-human CDR-H1 and CDR-H2 sequences with corresponding germline CDR sequence from said human VH; (4) identifying positions in CDR-L1, CDR-L2, CDR-L3, CDR-H1, and CDR-H2 where human germline residue is the same as, or different from, the corresponding non-human donor residue; and (5) generating the isolated humanized monoclonal antibody or antigen-binding fragment thereof by changing a non-human donor residue of the donor CDR-L1, CDR-L2, CDR-L3, CDR-H1, and CDR-H2 to the corresponding human germline residue if the human germline residue at the position is different from the corresponding non-human residue, wherein: (a) said isolated humanized monoclonal antibody or antigen-binding fragment thereof comprises (i) a VH domain comprising a human germline VH framework sequence from step (2) and a VL domain comprising a human germline VL framework sequence from step (2); and (ii) a CDR-L1, CDR-L2, CDR-L3, CDR-H1 and CDR-H2 from step (5); and (iii) a CDR-H3; (b) for each position within said CDR-L1, CDR-L2, CDR-L3, CDR-H1, and CDR-H2, the residue is either human germline residue from said human germline VL or VH, or corresponding residue from said non-human donor antibody; (c) said CDR-L1, CDR-L2, CDR-L3, CDR-H1, and CDR-H2 each comprises at least one more human germline residue as compared to the corresponding non-human donor CDR, (d) said CDR-L1, CDR-L2, CDR-L3, CDR-H1, and CDR-H2 each comprises at least one more non-human donor residue as compared to the corresponding human germline VH or VL CDR; and (e) for each position within CDR-H3, the residue is any one of the 20 natural amino acid residues.
 2. The antibody or antigen-binding fragment thereof of claim 1, wherein said human germline VH framework sequence comprises a VH3, VH1, or VH5 framework sequence.
 3. The antibody or antigen-binding fragment thereof of claim 1, wherein said human germline VH framework sequence comprises a VH germline consensus framework sequence.
 4. The antibody or antigen-binding fragment thereof of claim 1, wherein said human germline VH framework sequence comprises the VH framework sequence of any one of the consensus sequences listed in Table 2 and Table
 5. 5. The antibody or antigen-binding fragment thereof of claim 1, wherein said human germline VL framework sequence comprises a VK or V?, framework sequence.
 6. The antibody or antigen-binding fragment thereof of claim 1, wherein said human germline VL framework sequence comprises a VL germline consensus framework sequence.
 7. The antibody or antigen-binding fragment thereof of claim 1, wherein said human germline VL framework sequence comprises the VL framework sequence of any one of the human germline sequences listed in Table 3, Table 4 and Table
 6. 8. The antibody or antigen-binding fragment thereof of claim 1, wherein said human germline VH framework sequence is derived from the VH framework sequence of human germline DP54.
 9. The antibody or antigen-binding fragment thereof of claim 1, wherein said human germline VH framework sequence is derived from the VH framework sequence of SEQ ID NO:74.
 10. The antibody or antigen-binding fragment thereof of claim 1, wherein said human germline VL framework sequence is derived from a VK framework sequence.
 11. The antibody or antigen-binding fragment thereof of claim 1, wherein said human germline VL framework sequence is derived from the VL framework sequence of human germline DPK9.
 12. The antibody or antigen-binding fragment thereof of claim 1, wherein said human germline VL framework sequence is derived from the VL framework sequence of SEQ ID NO:144.
 13. The antibody or antigen-binding fragment thereof of claim 1, wherein the antibody or antigen-binding fragment binds said target antigen with a binding affinity (Kd) value that is equal or less than the binding affinity (Kd) value of said non-human donor antibody.
 14. The antibody or antigen-binding fragment thereof of claim 1, wherein the antibody or antigen-binding fragment maintains highly specific binding to said target antigen as compared to binding of said non-human donor antibody to said target antigen. 